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Hirani P, McDermott J, Rajeeve V, Cutillas PR, Jones JL, Pennington DJ, Wight TN, Santamaria S, Alonge KM, Pearce OM. Versican Associates with Tumor Immune Phenotype and Limits T-cell Trafficking via Chondroitin Sulfate. CANCER RESEARCH COMMUNICATIONS 2024; 4:970-985. [PMID: 38517140 PMCID: PMC10989462 DOI: 10.1158/2767-9764.crc-23-0548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 02/02/2024] [Accepted: 03/15/2024] [Indexed: 03/23/2024]
Abstract
Immunotherapies for cancers of epithelial origin have limited efficacy, and a growing body of evidence links the composition of extracellular matrix (ECM) with the likelihood of a favorable response to treatment. The ECM may be considered an immunologic barrier, restricting the localization of cytotoxic immune cells to stromal areas and inhibiting their contact with tumor cells. Identifying ECM components of this immunologic barrier could provide targets that whether degraded in situ may support antitumor immunity and improve immunotherapy response. Using a library of primary triple-negative breast cancer tissues, we correlated CD8+ T-cell tumor contact with ECM composition and identified a proteoglycan, versican (VCAN), as a putative member of the immunologic barrier. Our analysis reveals that CD8+ T-cell contact with tumor associates with the location of VCAN expression, the specific glycovariant of VCAN [defined through the pattern of posttranslational attachments of glycosaminoglycans (GAG)], and the cell types that produce the variant. In functional studies, the isomers of chondroitin sulfate presented on VCAN have opposing roles being either supportive or inhibiting of T-cell trafficking, and removal of the GAGs ameliorates these effects on T-cell trafficking. Overall, we conclude that VCAN can either support or inhibit T-cell trafficking within the tumor microenvironment depending on the pattern of GAGs present, and that VCAN is a major component of the ECM immunologic barrier that defines the type of response to immunotherapy. SIGNIFICANCE The response to immunotherapy has been poor toward solid tumors despite immune cells infiltrating into the tumor. The ECM has been associated with impacting T-cell infiltration toward the tumor and in this article we have identified VCAN and its structural modification, chondroitin sulfate as having a key role in T-cell invasion.
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Affiliation(s)
- Priyanka Hirani
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, United Kingdom
| | - Jacqueline McDermott
- Department of Histopathology, Imperial College Healthcare NHS Trust, London, United Kingdom
| | - Vinothini Rajeeve
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, United Kingdom
| | - Pedro R. Cutillas
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, United Kingdom
| | - J. Louise Jones
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, United Kingdom
| | - Daniel J. Pennington
- Centre for Immunobiology, Blizard Institute, Barts and the London Medical School, Queen Mary University of London, London, United Kingdom
| | - Thomas N. Wight
- Matrix Biology Program, Benaroya Research Institute at Virginia Mason, Seattle, Washington
| | - Salvatore Santamaria
- Department of Biochemical Sciences, School of Biosciences, Faculty of Health and Medical Sciences, Edward Jenner Building, University of Surrey, Surrey, United Kingdom
| | - Kimberly M. Alonge
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington
| | - Oliver M.T. Pearce
- Barts Cancer Institute, John Vane Science Centre, Queen Mary University of London, London, United Kingdom
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Qi J, Wu G, He M, Xu Y, Yang Z, Ding L, Wang Y, Zhang Z. CDK16 as a potential prognostic biomarker correlated with an immunosuppressive tumor microenvironment and benefits in enhancing the effectiveness of immunotherapy in human cancers. Aging (Albany NY) 2024; 16:1879-1896. [PMID: 38261737 PMCID: PMC10866429 DOI: 10.18632/aging.205465] [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: 09/22/2023] [Accepted: 12/14/2023] [Indexed: 01/25/2024]
Abstract
BACKGROUND Cyclin-Dependent Kinase 16 (CDK16) plays significant biological roles in various diseases. Nonetheless, its function in different cancer types and its relationship with the Tumor Immune Microenvironment (TIME) are still not well-understood. METHODS We analyzed the expression profile, genetic alterations, clinical features, and prognostic value of CDK16 in pan-cancer using data from The Cancer Genome Atlas, Genotype-Tissue Expression databases, and in vitro experiments. Additionally, the TIMER2 and ImmuCellAI databases were utilized to assess the correlation between CDK16 expression and immune cell infiltration levels. Finally, we examined the correlation between CDK16 and the response to immunotherapy using collected immunotherapy data. RESULTS CDK16 is notably overexpressed in pan-cancer and is a risk factor for poor prognosis in various cancers. Our findings reveal that CDK16 regulates not only cell cycle-related functions to promote cell proliferation but also the autoimmunity-related functions of the innate and adaptive immune systems, along with other immune-related signaling pathways. Moreover, CDK16 overexpression contributes to an immunosuppressive tumor microenvironment, extensively suppressing immune-related features such as the expression of immune-related genes and pathways, as well as the count of immune-infiltrating cells. Our analysis indicated that individuals with low CDK16 expression showed higher response rates to immune checkpoint inhibitors and longer overall survival compared to those with high CDK16 expression. CONCLUSIONS This study establishes CDK16 as a potential biomarker for predicting poor prognosis in a wide range of cancers. Its role in shaping the immunosuppressive tumor microenvironment and influencing the efficacy of immunotherapy highlights the urgent need for developing targeted therapies against CDK16, offering new avenues for cancer treatment and management.
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Affiliation(s)
- Juntao Qi
- Department of Urology, Shenzhen Hospital of Shanghai University of Traditional Chinese Medicine, Shenzhen 518000, China
- Department of Health Management, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan 410000, China
| | - Gujie Wu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, China
| | - Min He
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, China
| | - You Xu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, China
| | - Zheng Yang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, China
| | - Liang Ding
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226000, China
| | - Yan Wang
- Department of Urology, Shenzhen Hospital of Shanghai University of Traditional Chinese Medicine, Shenzhen 518000, China
| | - Zhi Zhang
- Department of Health Management, The First Hospital of Hunan University of Chinese Medicine, Changsha, Hunan 410000, China
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Maszota-Zieleniak M, Samsonov SA. Molecular Dynamics Simulation-Based Prediction of Glycosaminoglycan Interactions with Drug Molecules. Methods Mol Biol 2024; 2714:143-153. [PMID: 37676597 DOI: 10.1007/978-1-0716-3441-7_8] [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] [Indexed: 09/08/2023]
Abstract
Glycosaminoglycans (GAGs) are a class of long linear anionic periodic polysaccharides. Their biological activities are very broad including tissue remodeling, regulation of cell proliferation, cell migration, cell differentiation, participation in bacterial/viral infections, and immune response. They can interact with many important biomolecular partners in the extracellular matrix of the cell including small drug molecules. Recently, several GAG-bioactive small molecule complexes have been experimentally and theoretically studied. Some of these compounds in complexes with GAGs may potentially interfere with protein-GAG or peptide-GAG multimolecular systems affecting the processes of cellular differentiation or have anti-inflammatory, antiviral as well as antithrombotic effects. Although many studies have been conducted on GAG-drug complexes, the molecular mechanisms of the formation of such complexes are still poorly understood. At the same time, the complexity of their physicochemical properties renders the use of both experimental and computational methods to study these molecular systems challenging. Here, we present the molecular dynamics-based protocols successfully employed to in silico analyze GAG-small molecule interactions.
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Wu G, Zhou J, Ren H, Qin Y, Qian D, Hu Q, Xu P, Yu T, Ma H, Chen H, He M, Shi J. Unraveling the molecular crosstalk and immune landscape between COVID-19 infections and ischemic heart failure comorbidity: New insights into diagnostic biomarkers and therapeutic approaches. Cell Signal 2023; 112:110909. [PMID: 37777104 DOI: 10.1016/j.cellsig.2023.110909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/25/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Coronavirus disease 2019 (COVID-19), resulting from severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), remains a persistent global health concern. Evidence has highlighted a significant association between COVID-19 and ischemic heart failure (IHF), contributing to disease progression and increased mortality. This study identified diagnostic biomarkers for these comorbidities and elucidated disease progression's molecular mechanisms. METHODS We retrieved differentially expressed gene (DEG) data for COVID-19 and IHF from publicly available microarray and RNA-Seq datasets to investigate the underlying mechanisms and potential pathways associated with the co-occurrence of COVID-19 and IHF. By intersecting the results from the two diseases, we obtained diagnostic biomarkers using SVM-RFE and LASSO algorithms. Animal experiments and immunological analyses were conducted to help understand the association between SARS-CoV-2 and IHF in patients, enabling early diagnosis of disease progression. Finally, we analyzed the regulatory network of critical genes and identified potential drug compounds that could target the genetic links identified in our study. RESULTS 1974 common DEGs were identified between COVID-19 and IHF, contributing to disease progression and potential cancer risk by participating in immune and cancer-related pathways. In addition, we identified six hub genes (VDAC3, EIF2AK2, CHMP5, FTL, VPS4A, and CHMP4B) associated with the co-morbidity, and their diagnostic potential was confirmed through validation using relevant datasets and a mouse model. Functional enrichment analysis and examination of immune cell infiltration revealed immune dysregulation after disease progression. The comorbid hub genes exhibited outstanding immunomodulatory capacities. We also constructed regulatory networks tightly linked to both disorders, including transcription factors (TFs), miRNAs, and genes at both transcriptional and post-transcriptional levels. Finally, we identified 92 potential drug candidates to enhance the precision of anti-comorbidity treatment strategies. CONCLUSION Our study reveals a shared pathogenesis between COVID-19 and IHF, demonstrating that their coexistence exacerbates disease severity. By identifying and consolidating hub genes as pivotal diagnostic biomarkers for COVID-19 and IHF comorbidity, we have made significant advancements in understanding the underlying mechanisms of these conditions. Moreover, our study highlights dysregulated immunity and increased cancer risk in the advanced stages of disease progression. These findings offer novel perspectives for diagnosing and treating IHF progression during SARS-CoV-2 infection.
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Affiliation(s)
- Gujie Wu
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China; Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Jiabin Zhou
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Hefei Ren
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, Shanghai 200032, China
| | - Yiran Qin
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Diandian Qian
- Shanghai Medical College, Fudan University, Shanghai 200032, China; Department of Geriatrics, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Center for Evidence Based Medicine and Clinical Epidemiology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Qin Hu
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China; Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Peng Xu
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Tao Yu
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China; Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China; Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Huiyun Ma
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Hongyu Chen
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Min He
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China
| | - Jiayu Shi
- Department of Cardiology, Affiliated Hospital of Nantong University, Nantong 226000, China.
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Hu Q, Wu G, Ma H, Zhang J, Yang Z. Signal sequence receptor subunit 3: A novel indicator of immunosuppressive tumor microenvironment and clinical benefits from immunotherapy. Cell Signal 2023; 111:110871. [PMID: 37652395 DOI: 10.1016/j.cellsig.2023.110871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 07/25/2023] [Accepted: 08/25/2023] [Indexed: 09/02/2023]
Abstract
BACKGROUND Signal sequence receptor subunit 3 (SSR3), a translocation-associated protein complex, plays a vital role in various diseases. However, its involvement in human cancers remains unclear. METHODS We conducted a comprehensive analysis by integrating data from multiple sources, including the Cancer Genome Atlas, Cancer Cell Lineage Encyclopedia, Genotype Tissue Expression, Human Protein Atlas, cBioPortal, TIMER, and ImmuCellAI. Additionally, we incorporated data from a clinical trial, two immunotherapy cohorts, and in vitro experiments to investigate SSR3's impact on cancer prognosis and immune response. RESULTS Our findings revealed a significant correlation between elevated SSR3 expression and unfavorable prognosis across various cancer types. Amplification is the most common genetic alteration in SSR3. Furthermore, functional enrichment analysis highlighted SSR3's regulatory role in promoting proliferation. In addition, SSR3 also serves as a pivotal mediator bridging the innate and adaptive immune systems and several related signaling pathways. Moreover, the correlation of SSR3 expression with tumor mutation burden in five cancer types, as well as with microsatellite instability in nine cancer types, suggests the potential of SSR3 as a predictive marker for immunotherapy response. To validate this hypothesis, we examined data from patients who underwent immunotherapy treatment. Our analysis revealed that individuals with low SSR3 expression demonstrated higher response rates to immune checkpoint inhibitors and longer overall survival compared to those with high SSR3 expression. CONCLUSIONS Our study identifies SSR3 as a potential oncogene in humans, implicated in both tumorigenesis and cancer immunity. Elevated SSR3 expression is indicative of an immunosuppressive tumor microenvironment. Therefore, SSR3 holds promise as a potential prognostic biomarker and a target for immunotherapy in cancer treatment.
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Affiliation(s)
- Qin Hu
- Department of Respiratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226000, China; Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226000, China
| | - Gujie Wu
- Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Huiyun Ma
- Department of Respiratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226000, China; Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226000, China
| | - Jiaxin Zhang
- Department of Cardiothoracic Surgery, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226000, China
| | - Zheng Yang
- Department of Respiratory Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226000, China.
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Chen Y, Zou P, Bu C, Jiang Q, Xue L, Bao J, Zhang T. Upregulated CXCL8 in placenta accreta spectruma regulates the migration and invasion of HTR-8/SVneo cells. Mol Biol Rep 2023; 50:8189-8199. [PMID: 37563526 DOI: 10.1007/s11033-023-08669-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023]
Abstract
BACKGROUND Placenta accreta spectrum (PAS) is mainly characterized by excessive invasion of the uterine muscle layer accompanied by a large number of foreign blood vessels, leading to severe bleeding during and after delivery. However, the mechanism of excessive invasion of nutrient cells in placenta accreta is currently unclear. METHODS We performed RNA sequencing of 6 PAS patients and 4 control donors, coupled with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. The mRNA and protein expression of C-X-C motif ligand 8 (CXCL8) in the placental tissue was measured by qRT‒PCR, immunohistochemical staining and Western blotting. HTR-8/SVneo human villous trophoblast Neo cells were used for in vitro investigation of cell migration and invasion as well as the expression level of CXCL8. RESULTS A total of 1120 differentially expressed mRNAs were identified in PAS patients. Moreover, GO and KEGG analyses indicated that the differentially expressed mRNAs were most closely associated with immune system processes, biological adhesion and Wnt signaling pathway. The CXCL8 mRNA and protein levels in PAS tissue were significantly higher than those in normal placental tissue. Forced overexpression of CXCL8 significantly increased the migration and invasion of HTR-8/SVneo cells, accompanied by the upregulation of matrix metalloproteinase-2 and matrix metalloproteinase-9 and the downregulation of E-cadherin, which was reversed by knockdown of CXCL8. CONCLUSIONS CXCL8 was highly expressed in PAS, and knockdown of CXCL8 suppressed the migration and invasion of HTR-8/SVneo cells, suggesting its potential as a diagnostic and therapeutic target for PAS.
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Affiliation(s)
- Yuejuan Chen
- Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, 214002, China
| | - Ping Zou
- Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, 214002, China
| | - Chaozhi Bu
- Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, 214002, China
| | - Qianying Jiang
- Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, 214002, China
| | - Lili Xue
- Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, 214002, China
| | - Junfeng Bao
- Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, 214002, China.
| | - Ting Zhang
- Wuxi Maternity and Child Health Care Hospital, Women's Hospital of Jiangnan University, Jiangnan University, Wuxi, 214002, China.
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Wu G, Dong Y, Hu Q, Ma H, Xu Q, Xu K, Chen H, Yang Z, He M. HGH1 and the immune landscape: a novel prognostic marker for immune-desert tumor microenvironment identification and immunotherapy outcome prediction in human cancers. Cell Cycle 2023; 22:1969-1985. [PMID: 37811868 PMCID: PMC10761050 DOI: 10.1080/15384101.2023.2260163] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 09/06/2023] [Indexed: 10/10/2023] Open
Abstract
HGH1 homolog, a protein-coding gene, plays a crucial role in human growth and development. However, its role in human cancer remains unclear. For the first time, this study comprehensively evaluated the potential involvement of HGH1 in cancer prognosis and immunological function. To achieve this, data from various databases, including The Cancer Genome Atlas, Genotype Tissue Expression, Cancer Cell Lineage Encyclopedia, Human Protein Atlas, cBioPortal, Tumor Immune Estimation Resource and Immune Cell Abundance Identifier, were collated, as well as from one large clinical study, three immunotherapy cohorts and in vitro experiments. This study aims to elucidate the role of HGH1 expression in cancer prognosis and immune response. Our findings revealed a significant association between increased HGH1 expression and a worse prognosis across various cancer types. Predominantly, copy number variations were identified as the most common genetic mutations. Additionally, HGH1 was observed to not only regulate cell cycle-related functions to promote cell proliferation but also influence autoimmunity-related functions within both the innate and adaptive immune systems, along with other relevant immune-related signaling pathways. Gene set enrichment analysis and gene set variation analysis were used to substantiate these findings. HGH1 overexpression contributed to an immune-deficient (immune-desert) tumor microenvironment, which was characterized by a significant expression of immune-related features such as immune-related gene and pathway expression and the number of immune-infiltrating cells. Furthermore, the correlation between HGH1 expression and tumor mutational burden in four cancers and microsatellite instability in eight cancers was observed. This suggests that HGH1 has potential as an immunotherapeutic target. Immunotherapy data analysis supports this notion, demonstrating that patients with low HGH1 expression treated with immune checkpoint inhibitors exhibit improved survival rates and a higher likelihood of responding to immunotherapy than patients with high HGH1 expression. Collectively, these findings highlight the significant role of HGH1 in human cancers, illuminating its involvement in tumorigenesis and cancer immunity. Elevated HGH1 expression was identified to be indicative of an immune-desert tumor microenvironment. Consequently, the targeting of HGH1, particularly in combination with immune checkpoint inhibitor therapy, holds promise for enhancing therapeutic outcomes in patients with cancer.
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Affiliation(s)
- Gujie Wu
- Department of Thoracic Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
- Shanghai Medical College, Fudan University, Shanghai, China
| | - Yipeng Dong
- School of Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Qin Hu
- Shanghai Medical College, Fudan University, Shanghai, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Huiyun Ma
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Qun Xu
- School of Medicine, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Kun Xu
- Department of Chemotherapy, Jiangsu Cancer Hospital, Nanjing Medical University, Nanjing, China
| | - Hongyu Chen
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zheng Yang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Min He
- Shanghai Medical College, Fudan University, Shanghai, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
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Wu G, Ren H, Hu Q, Ma H, Chen H, Zhou L, Xu K, Ding L. The circadian rhythm key gene ARNTL2: a novel prognostic biomarker for immunosuppressive tumor microenvironment identification and immunotherapy outcome prediction in human cancers. Front Immunol 2023; 14:1115809. [PMID: 37275880 PMCID: PMC10237319 DOI: 10.3389/fimmu.2023.1115809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/03/2023] [Indexed: 06/07/2023] Open
Abstract
Background Aryl hydrocarbon receptor nuclear translocator-like 2 (ARNTL2) belongs to the b HLH- PAS domain transcription factor family and is one of the key clock genes that control the circadian rhythm. ARNTL2 plays an important role in human biological functions. However, its role in various tumors, especially in the tumor immune microenvironment (TIME) and immunotherapy, remains unclear. Methods We integrated data from cancer patients from multiple databases, including the Cancer Genome Atlas, Cancer Cell Lineage Encyclopedia, Genotype Tissue Expression, Human Protein Atlas, cBioPortal, TIMER, and ImmuCellAI, with data from a large clinical study, three immunotherapy cohorts, and in vitro experiments to investigate the involvement of ARNTL2 expression in cancer prognosis and immune response. Results ARNTL2 displayed abnormal expression within most malignant tumors, and is significantly associated with poorer survival and pathologic staging. Through gene-set enrichment analysis (GSEA) and gene-set variation analysis (GSVA), we found that ARNTL2 not only regulates cell cycle-related functions to promote cell proliferation but also regulates autoimmunity-related functions of the innate and adaptive immune systems, and other immune-related signaling pathways. In addition, ARNTL2 overexpression contributes to an immunosuppressive tumor microenvironment that plays a key role in immunosuppression-related features, such as the expression of immunosuppression-related genes and pathways and the number of immunosuppressive-infiltrating cells, including regulatory T cells (Tregs), tumor-associated macrophages (TAMs), and cancer-associated fibroblasts (CAFs). The group of patients with low ARNTL2 expression who received immune checkpoint inhibitors (ICI) therapy had better response rates and longer survival when compared to those with high ARNTL2 expression. Conclusion The findings of this study suggest that ARNTL2 is a potential human oncogene that plays an important role in tumorigenesis and cancer immunity. Elevated ARNTL2 expression indicates an immunosuppressive tumor microenvironment. Targeting ARNTL2 in combination with ICI therapy could bring more significant therapeutic benefits to patients with cancer. Our study sheds light on the remarkable potential of ARNTL2 in tumor immunity and provides a novel perspective for anti-tumor strategies.
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Affiliation(s)
- Gujie Wu
- Department of Respiratory medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Hefei Ren
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Qin Hu
- Department of Respiratory medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Huiyun Ma
- Department of Respiratory medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Hongyu Chen
- Department of Respiratory medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Lin Zhou
- Department of Respiratory medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
| | - Kun Xu
- Department of Chemotherapy, Jiangsu Cancer Hospital, Nanjing Medical University, Nanjing, China
| | - Liang Ding
- Department of Respiratory medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu, China
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Li Z, Huang L, Li J, Yang W, Li W, Long Q, Dai X, Wang H, Du G. Immunological role and prognostic value of the SKA family in pan-cancer analysis. Front Immunol 2023; 14:1012999. [PMID: 37180139 PMCID: PMC10169755 DOI: 10.3389/fimmu.2023.1012999] [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: 08/06/2022] [Accepted: 02/27/2023] [Indexed: 05/15/2023] Open
Abstract
Background The spindle and kinetochore associated (SKA) complex, which plays important roles in proper chromosome segregation during mitosis by maintaining the stabilization of kinetochore-spindle microtubule attachment during mitosis, has recently been reported to exert regulatory effects on the initiation and progression of various human cancer types. Nevertheless, the prognostic significance and immune infiltration of the SKA family across cancers have not been well elucidated. Methods Using data from three large public datasets, including The Cancer Genome Atlas, Genotype-Tissue Expression, and Gene Expression Omnibus databases, a novel scoring system (termed the SKA score) was developed to quantify the SKA family level across cancers. We then evaluated the prognostic impact of the SKA score on survival and assessed the effect of the SKA score on immunotherapy at the pan-cancer level using multiomics bioinformatic analyses. The correlation of the SKA score and the tumor microenvironment (TME) was also explored in depth. Potential small molecular compounds and chemotherapeutic agents were assessed by CTRP and GDSC analyses. Immunohistochemistry was performed to verify the expression of the SKA family genes. Results Our results demonstrated a close correlation between the SKA score and tumor development and prognosis in multiple cancers. The SKA score was positively related to cell cycle pathways and DNA replication across cancers, such as E2F targets, the G2M checkpoint, MYC targets V1/V2, mitotic spindles and DNA repair. Additionally, the SKA score was negatively related to the infiltration of various immune cells with antitumor effects in the TME. In addition, the potential value of the SKA score was identified to predict immunotherapy response for melanoma and bladder cancer. We also demonstrated a correlation between SKA1/2/3 and the response to drug treatment across cancers and the promising potential of the SKA complex and its genes as therapeutic targets in cancer. Immunohistochemistry demonstrated that the expression differences of SKA1/2/3 were significant between the breast cancer group and the paracancerous group. Conclusion The SKA score plays a critical role in 33 cancer types and is highly related to tumor prognosis. Patients with elevated SKA scores have a clear immunosuppressive TME. The SKA score may serve as a predictor for patients receiving anti-PD-1/L1 therapy.
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Affiliation(s)
- Zhengtian Li
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Lanying Huang
- Department of Rehabilitation Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Jiachen Li
- Department of Gastrointestinal and Gland Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wenkang Yang
- Department of Gastrointestinal and Gland Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Weichao Li
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Qiuzhong Long
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xinyu Dai
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Hongtao Wang
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Gang Du
- Department of Bone and Joint Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Bi C, Wang Z, Xiao Y, Zhao Y, Guo R, Xiong L, Ji Z, Li Y, Li Q, Qin C. I kappa B kinase interacting protein as a promising biomarker in pan-cancer: A multi-omics analysis. Front Genet 2023; 14:1138137. [PMID: 36999060 PMCID: PMC10047260 DOI: 10.3389/fgene.2023.1138137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/02/2023] [Indexed: 03/18/2023] Open
Abstract
Background: Human chromosome 12 contains I kappa B kinase interacting protein (IKBIP) is also commonly known as IKIP. The involvement of IKBIP in the growth of tumors has only been discussed in a small number of publications.Purpose: To explore the role that IKBIP plays in the development of a wide variety of neoplasms, as well as the tumor immunological microenvironment.Methods: UALCAN, HPA, Genotype Tissue Expression, Cancer Genome Maps, and other datasets were used to analyze IKBIP expression. We thoroughly investigated the predictive importance of IKBIP in pan-cancer, clinical traits, and genetic anomalies. We studied whether there is a link between IKBIP and immune-related genes, microsatellite instability (MSI), and the incidence of tumor mutational burden (TMB). The link between immune cell infiltration and IKBIP expression was examined using data on immune cell infiltration from ImmuCellAI, TIMER2, and earlier studies. Finally, gene set enrichment analysis (GSEA) was performed to determine the signaling pathways associated with IKBIP.Results: IKBIP is highly expressed in most cancers and is negatively associated with the prognosis of several major cancer types. Furthermore, IKBIP expression was linked to TMB in 13 cancers and MSI in seven cancers. Additionally, IKBIP is associated with numerous immunological and cancer-promoting pathways. Simultaneously, various cancer types have unique tumor-infiltrating immune cell profiles.Conclusion: IKBIP has the potential to act as a pan-cancer oncogene and is crucial for both carcinogenesis and cancer immunity. Elevated IKBIP expression implies an immunosuppressive environment and may be used as a prognostic biomarker and therapeutic target.
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Lei W, Jia L, Wang Z, Liang Z, Aizhen Z, Liu Y, Tian Y, Zhao L, Chen Y, Shi G, Yang Z, Yang Y, Xu X. CC chemokines family in fibrosis and aging: From mechanisms to therapy. Ageing Res Rev 2023; 87:101900. [PMID: 36871782 DOI: 10.1016/j.arr.2023.101900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/21/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023]
Abstract
Fibrosis is a universal aging-related pathological process in the different organ, but is actually a self-repair excessive response. To date, it still remains a large unmet therapeutic need to restore injured tissue architecture without detrimental side effects, due to the limited clinical success in the treatment of fibrotic disease. Although specific organ fibrosis and the associated triggers have distinct pathophysiological and clinical manifestations, they often share involved cascades and common traits, including inflammatory stimuli, endothelial cell injury, and macrophage recruitment. These pathological processes can be widely controlled by a kind of cytokines, namely chemokines. Chemokines act as a potent chemoattractant to regulate cell trafficking, angiogenesis, and extracellular matrix (ECM). Based on the position and number of N-terminal cysteine residues, chemokines are divided into four groups: the CXC group, the CX3C group, the (X)C group, and the CC group. The CC chemokine classes (28 members) is the most numerous and diverse subfamily of the four chemokine groups. In this Review, we summarized the latest advances in the understanding of the importance of CC chemokine in the pathogenesis of fibrosis and aging and discussed potential clinical therapeutic strategies and perspectives aimed at resolving excessive scarring formation.
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Affiliation(s)
- Wangrui Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, 710069, China
| | - Liyuan Jia
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, 710069, China
| | - Zheng Wang
- Department of Cardiothoracic Surgery, Central Theater Command General Hospital of Chinese People's Liberation Army, Wuhan, 430064, China
| | - Zhenxing Liang
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Zhengzhou University, 1 Jianshe East, Zhengzhou 450052, China
| | - Zhao Aizhen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, 710069, China
| | - Yanqing Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, 710069, China
| | - Ye Tian
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, 710069, China
| | - Lin Zhao
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Yawu Chen
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Guangyong Shi
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Zhi Yang
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China
| | - Yang Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. Faculty of Life Sciences and Medicine, Northwest University, Xi'an, 710069, China.
| | - Xuezeng Xu
- Department of Cardiovascular Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, 710032, China.
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Xie J, Zhang J, Tian W, Zou Y, Tang Y, Zheng S, Wong CW, Deng X, Wu S, Chen J, Mo Y, Xie X. The Pan-Cancer Multi-Omics Landscape of FOXO Family Relevant to Clinical Outcome and Drug Resistance. Int J Mol Sci 2022; 23:ijms232415647. [PMID: 36555288 PMCID: PMC9778770 DOI: 10.3390/ijms232415647] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022] Open
Abstract
The forkhead box O (FOXO) transcription factors (TFs) family are frequently mutated, deleted, or amplified in various human cancers, making them attractive candidates for therapy. However, their roles in pan-cancer remain unclear. Here, we evaluated the expression, prognostic value, mutation, methylation, and clinical features of four FOXO family genes (FOXO1, FOXO3, FOXO4, and FOXO6) in 33 types of cancers based on the Cancer Genome Atlas (TCGA) and Genotype Tissue Expression (GTEx) databases. We used a single sample gene set enrichment analysis (ssGSEA) algorithm to establish a novel index called "FOXOs score". Moreover, we investigated the association between the FOXOs score and tumor microenvironment (TME), the responses to multiple treatments, along with drug resistance. We found that the FOXO family genes participated in tumor progression and were related to the prognosis in various types of cancer. We calculated the FOXOs score and found that it was significantly correlated with multiple malignant pathways in pan-cancer, including Wnt/beta-catenin signaling, TGF-beta signaling, and hedgehog signaling. In addition, the FOXOs score was also associated with multiple immune-related characteristics. Furthermore, the FOXOs score was sensitive for predicting the efficacy of diverse treatments in multiple cancers, especially immunotherapy. In conclusion, FOXO family genes were vital in pan-cancer and were strongly correlated with the TME. A high FOXOs score indicated an excellent immune-activated TME and sensitivity to multiple treatments. Hence, the FOXOs score might potentially be used as a biomarker in patients with a tumor.
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Affiliation(s)
- Jindong Xie
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Junsheng Zhang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Wenwen Tian
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Yutian Zou
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Yuhui Tang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Shaoquan Zheng
- Breast Disease Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
| | - Chau-Wei Wong
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Song Wu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Junxin Chen
- Department of Endocrinology and Diabetes Center, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510060, China
| | - Yunxian Mo
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Correspondence: (Y.M.); (X.X.); Tel.: +86-13924277788 (X.X.); Fax: +86-20-87343805 (X.X.)
| | - Xiaoming Xie
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
- Correspondence: (Y.M.); (X.X.); Tel.: +86-13924277788 (X.X.); Fax: +86-20-87343805 (X.X.)
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Li Y, Fu W, Geng Z, Song Y, Yang X, He T, Wu J, Wang B. A pan-cancer analysis of the oncogenic role of ribonucleotide reductase subunit M2 in human tumors. PeerJ 2022; 10:e14432. [PMID: 36518297 PMCID: PMC9744174 DOI: 10.7717/peerj.14432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/31/2022] [Indexed: 11/29/2022] Open
Abstract
Background Recent studies have identified ribonucleotide reductase subunit M2 (RRM2) as a putative promoter of tumors. However, no systematic analysis of its carcinogenicity has been conducted. Methods The potential functions of RRM2 in various tumor types were investigated using data from the Genotype-Tissue Expression (GTEx), the Clinical Proteomic Tumor Analysis Consortium (CPTAC), the Cancer Genome Atlas (TCGA), the Human Protein Atlas (HPA), cBioPortal, GEPIA, String, and Gene Set Enrichment Analysis (GSEA). We analyzed the difference in mRNA and protein expression, pathological stage, survival, mutation, tumor microenvironment (TME), and immune cell infiltration in relation to RRM2. Meanwhile, using TCGA and the Tumor Immune Estimation Resource 2 (TIMER 2), the associations between RRM2 expression, immune infiltration, and immune-related genes were assessed. Additionally, CCK-8, Edu and RT-PCR assays were used to validate that RRM2 acts as an oncogene in liver cancer cells and its association with HBx. A cohort of liver hepatocellular carcinoma (LIHC) patients (n=154) from Huashan Hospital was analyzed for the expression of RRM2 and the association between RRM2 and immune infiltration. Results Using the GTEx and TCGA databases, we discovered that 28 tumors expressed RRM2 at significantly higher levels than the corresponding normal tissues. Increased RRM2 expression may be predictive of a poor overall survival (OS) in patients with seven different cancers. GO, KEGG, and GSEA analyses revealed that the biological process of RRM2 was associated with the regulation of carcinogenic processes and immune pathways in a variety of tumor types. The expression of RRM2 was highly correlated with maker genes involved in immune activation and immunosuppression, immune checkpoints, DNA mismatch repair system (MMR), and the infiltration levels of Tregs and macrophages (TAMs), suggesting that the carcinogenic effect of RRM2 may be achieved by regulating immune related genes. Moreover, as demonstrated by CCK-8 and Edu assays, RRM2 was an oncogene in liver cancer cells. We confirmed for the first time that RRM2 was significantly upregulated by HBx, suggesting that RRM2 may be a key regulator of LIHC induced by HBV. IHC analysis validated the upregulated expression of RRM2 protein and its correlation with immune infiltration makers in a LIHC patient cohort. Conclusion RRM2 may be a valuable molecular biomarker for predicting prognosis and immunotherapeutic efficacy in pan-cancer, particularly in LIHC.
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Affiliation(s)
- Yaqun Li
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhuan Fu
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Zikai Geng
- Pharmacy School, Binzhou Medical University, Shandong, China
| | - Yun Song
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Xionggang Yang
- Department of Orthopedic Surgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Tianye He
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Jian Wu
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
| | - Bin Wang
- Department of Pharmacy, Huashan Hospital, Fudan University, Shanghai, China
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Xu M, Zhang T, Xia R, Wei Y, Wei X. Targeting the tumor stroma for cancer therapy. Mol Cancer 2022; 21:208. [PMID: 36324128 PMCID: PMC9628074 DOI: 10.1186/s12943-022-01670-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/13/2022] [Accepted: 10/13/2022] [Indexed: 11/06/2022] Open
Abstract
Tumors are comprised of both cancer cells and surrounding stromal components. As an essential part of the tumor microenvironment, the tumor stroma is highly dynamic, heterogeneous and commonly tumor-type specific, and it mainly includes noncellular compositions such as the extracellular matrix and the unique cancer-associated vascular system as well as a wide variety of cellular components including activated cancer-associated fibroblasts, mesenchymal stromal cells, pericytes. All these elements operate with each other in a coordinated fashion and collectively promote cancer initiation, progression, metastasis and therapeutic resistance. Over the past few decades, numerous studies have been conducted to study the interaction and crosstalk between stromal components and neoplastic cells. Meanwhile, we have also witnessed an exponential increase in the investigation and recognition of the critical roles of tumor stroma in solid tumors. A series of clinical trials targeting the tumor stroma have been launched continually. In this review, we introduce and discuss current advances in the understanding of various stromal elements and their roles in cancers. We also elaborate on potential novel approaches for tumor-stroma-based therapeutic targeting, with the aim to promote the leap from bench to bedside.
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Affiliation(s)
- Maosen Xu
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041, Chengdu, Sichuan, PR China
| | - Tao Zhang
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041, Chengdu, Sichuan, PR China
| | - Ruolan Xia
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041, Chengdu, Sichuan, PR China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041, Chengdu, Sichuan, PR China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, West China Hospital, National Clinical Research Center for Geriatrics, Sichuan University, No. 17, Block 3, Southern Renmin Road, 610041, Chengdu, Sichuan, PR China.
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15
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Jurj A, Ionescu C, Berindan-Neagoe I, Braicu C. The extracellular matrix alteration, implication in modulation of drug resistance mechanism: friends or foes? J Exp Clin Cancer Res 2022; 41:276. [PMID: 36114508 PMCID: PMC9479349 DOI: 10.1186/s13046-022-02484-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 09/01/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractThe extracellular matrix (ECM) is an important component of the tumor microenvironment (TME), having several important roles related to the hallmarks of cancer. In cancer, multiple components of the ECM have been shown to be altered. Although most of these alterations are represented by the increased or decreased quantity of the ECM components, changes regarding the functional alteration of a particular ECM component or of the ECM as a whole have been described. These alterations can be induced by the cancer cells directly or by the TME cells, with cancer-associated fibroblasts being of particular interest in this regard. Because the ECM has this wide array of functions in the tumor, preclinical and clinical studies have assessed the possibility of targeting the ECM, with some of them showing encouraging results. In the present review, we will highlight the most relevant ECM components presenting a comprehensive description of their physical, cellular and molecular properties which can alter the therapy response of the tumor cells. Lastly, some evidences regarding important biological processes were discussed, offering a more detailed understanding of how to modulate altered signalling pathways and to counteract drug resistance mechanisms in tumor cells.
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16
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Wu G, Chen M, Ren H, Sha X, He M, Ren K, Qi J, Lin F. AP3S1 is a Novel Prognostic Biomarker and Correlated With an Immunosuppressive Tumor Microenvironment in Pan-Cancer. Front Cell Dev Biol 2022; 10:930933. [PMID: 35874816 PMCID: PMC9304770 DOI: 10.3389/fcell.2022.930933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Adaptor-related protein complex 3, sigma one subunit (AP3S1) is one of the encoding subunits of the adaptor complex AP-3. However, its role in various tumor types and relationship with the tumor immune microenvironment (TIME) remains unclear.Methods: AP3S1 expression was analyzed using datasets from The Cancer Genome Atlas, Genotype-Tissue Expression, UALCAN, and HPA databases. Then, we performed a systematic analysis of the genetic alterations, clinical features, and prognostic value of AP3S1 in pan-cancer. Gene set enrichment analysis (GSEA) and gene set variation analysis (GSVA) were used to identify the signaling pathways associated with AP3S1. The correlation between immune cell infiltration and AP3S1 expression was analyzed using immune cell infiltration data from the ImmuCellAI, TIMER2, and a previous study. Finally, we analyzed the association of AP3S1 with tumor mutational burden (TMB), microsatellite instability (MSI), and immune-related genes.Results: We found AP3S1 overexpression in most tumors and a significant association with low survival rates. GSEA and GSVA results show that AP3S1 is involved in tumor progression and associated with immune pathways in different tumor types. We also found that AP3S1 expression was positively correlated with the level of infiltration of immunosuppressive cells (tumor-associated macrophages, cancer-associated fibroblasts, Tregs) and negatively correlated with immune killer cells, including NK cells and CD8+ T cells, in pan-cancer. The expression of AP3S1 could affect TMB and MSI in various cancers. In addition, AP3S1 was positively correlated with most immunosuppressive genes, including PD-1, PD-L1, CTLA4, LAG3 and TIGIT in most cancer types.Conclusion: Our study reveals that AP3S1 is a potential pan-cancer oncogene and plays an essential role in tumorigenesis and cancer immunity. Elevated expression of AP3S1 indicates an immunosuppressive microenvironment and can be used as a potential prognostic biomarker and a target for immunotherapy.
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Affiliation(s)
- Gujie Wu
- Department of Urology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Mianxiong Chen
- Department of Urology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Hefei Ren
- Department of Laboratory Medicine, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Xinyu Sha
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Min He
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Kuan Ren
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Juntao Qi
- Department of Urology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
- *Correspondence: Juntao Qi, ; Feng Lin,
| | - Feng Lin
- Department of Urology, Shenzhen Traditional Chinese Medicine Hospital, Guangzhou University of Chinese Medicine, Shenzhen, China
- *Correspondence: Juntao Qi, ; Feng Lin,
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17
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Wu G, He M, Yin X, Wang W, Zhou J, Ren K, Chen X, Xue Q. The Pan-Cancer Landscape of Crosstalk Between TRP Family and Tumour Microenvironment Relevant to Prognosis and Immunotherapy Response. Front Immunol 2022; 13:837665. [PMID: 35493463 PMCID: PMC9043495 DOI: 10.3389/fimmu.2022.837665] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/17/2022] [Indexed: 01/24/2023] Open
Abstract
Background Transient Receptor Potential (TRP) channel is a kind of channel protein widely distributed in peripheral and central nervous system. They can be regulated by natural aromatic substances and serve as a therapeutic target for many diseases. However, the role and function of the TRP family genes in tumours remain unclear. Methods Gene alterations (mutation, copy number, methylation), expression, clinical features, and prognostic value of the TRP family genes were evaluated in pan-cancer using data from The Cancer Genome Atlas and Genotype-Tissue Expression databases. TRP score was calculated by the ssGSEA function of the R package "GSVA". The association of TRP score and the tumour microenvironment (TME), especially the tumour immune microenvironment (TIME), along with immunotherapy response were explored in-depth. Results TRP family genes were involved in tumour progression and highly associated with poor prognosis in a variety of cancers. TRP score was positively associated with malignant pathways in pan-cancer, such as IL6-JAK-STAT3 signalling, interferon-gamma response, and inflammatory response. All pathways were closely associated with TIME. Elevated TRP score also correlated with multiple immune-related characteristics of the TIME in pan-cancer. Moreover, the TRP score was a predictive biomarker for immune checkpoint inhibitor (ICI) treatments in patients with tumours. Conclusions TRP family genes play a key role in pan-cancer and are closely associated with TME. Patients with high TRP scores have excellent immune-activated TIME and immunotherapy sensitivity. Therefore, the TRP score could be a potential biomarker for patients with tumours treated with ICI.
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Affiliation(s)
- Gujie Wu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Min He
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xi Yin
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Wenmaio Wang
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Jiabin Zhou
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Kuan Ren
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, China
| | - Xinming Chen
- Cardiothoracic Surgery Department, Affiliated Hospital of Nantong University, Nantong, China
| | - Qun Xue
- Cardiothoracic Surgery Department, Affiliated Hospital of Nantong University, Nantong, China
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Molecular Dynamics Approaches Dissect Molecular Mechanisms Underlying Methylene Blue-Glycosaminoglycan Interactions. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092654. [PMID: 35566005 PMCID: PMC9105714 DOI: 10.3390/molecules27092654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/12/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Glycosaminoglycans (GAGs) are a class of periodic anionic linear polysaccharides involved in a number of biologically relevant processes in the extracellular matrix via interactions with various types of molecules including proteins, peptides and small organic molecules. The metachromatic dye methylene blue (MB) is a GAG binding agent. This molecule possesses a tricyclic, monocationic phenothiazine ring system, while the terminal methyl groups attached to the nitrogen atoms bear the most positive charges of the cation and, therefore, represent potential binding sites for negatively charged GAGs. In this study, we rigorously explored molecular mechanisms underlying these interactions for several GAG types: heparin, heparan and chondroitin sulfates. We found that GAG-MB interactions are predominantly electrostatically driven, with the particularly important role of sulfate groups. MB oligomeric stack formation was favored in the presence of GAGs. Furthermore, the impact of MB binding on the conformation of GAGs was also evaluated. The novel results allow for better quantitative analytics of GAG composition in the studied biochemical systems using MB dye as a GAG-specific marker. Our data add to the knowledge on small molecule-GAG interactions and could be potentially useful for novel developments in drug design and putative disease therapies in which GAGs are involved.
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Duckworth BC, Qin RZ, Groom JR. Spatial determinates of effector and memory CD8 + T cell fates. Immunol Rev 2021; 306:76-92. [PMID: 34882817 DOI: 10.1111/imr.13044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 11/06/2021] [Indexed: 12/17/2022]
Abstract
The lymph node plays a critical role in mounting an adaptive immune response to infection, clearance of foreign pathogens, and cancer immunosurveillance. Within this complex structure, intranodal migration is vital for CD8+ T cell activation and differentiation. Combining tissue clearing and volumetric light sheet fluorescent microscopy of intact lymph nodes has allowed us to explore the spatial regulation of T cell fates. This has determined that short-lived effector (TSLEC ) are imprinted in peripheral lymph node interfollicular regions, due to CXCR3 migration. In contrast, stem-like memory cell (TSCM ) differentiation is determined in the T cell paracortex. Here, we detail the inflammatory and chemokine regulators of spatially restricted T cell differentiation, with a focus on how to promote TSCM . We propose a default pathway for TSCM differentiation due to CCR7-directed segregation of precursors away from the inflammatory effector niche. Although volumetric imaging has revealed the consequences of intranodal migration, we still lack knowledge of how this is orchestrated within a complex chemokine environment. Toward this goal, we highlight the potential of combining microfluidic chambers with pre-determined complexity and subcellular resolution microscopy.
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Affiliation(s)
- Brigette C Duckworth
- Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, Vic, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Vic, Australia
| | - Raymond Z Qin
- Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, Vic, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Vic, Australia
| | - Joanna R Groom
- Division of Immunology, Walter and Eliza Hall Institute of Medical Research, Parkville, Vic, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Vic, Australia
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20
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Zhong A, Chen T, Xing Y, Pan X, Shi M. FUCA2 Is a Prognostic Biomarker and Correlated With an Immunosuppressive Microenvironment in Pan-Cancer. Front Immunol 2021; 12:758648. [PMID: 34745134 PMCID: PMC8565374 DOI: 10.3389/fimmu.2021.758648] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/07/2021] [Indexed: 11/23/2022] Open
Abstract
Background The expression of Fucosidase, alpha-L-2 (FUCA2) varies across tumors. However, its role in various tumor types and relationship with the tumor immune microenvironment (TIME) is poorly defined. Methods We analyzed profiles of FUCA2 expression using datasets from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases. Next, gene alteration, clinical characteristics and prognostic values of FUCA2 were elucidated based on TCGA pan-cancer data. This was followed by gene set enrichment analysis by R software. Relationships between FUCA2 expression and immune infiltration and immune-related genes were also evaluated. Moreover, the association of immune cell infiltration with FUCA2 expression was evaluated across three different sources of immune cell infiltration data, namely the TIMER online, ImmuCellAI databases, as well as a published study. In addition, MTT assays was also conducted to validate the oncogene role of FUCA2 in lung cancer cells. Results FUCA2 was upregulated in most tumors, and this was significantly associated with poor survival rates. Gene set enrichment analysis uncovered that FUCA2 correlated with immune pathways in different tumor types. FUCA2 expression was positively related to tumor associated macrophages (TAMs), especially M2-like TAMs. Moreover, FUCA2 level showed a positive relationship with most immunosuppression genes, including programmed death-ligand 1 (PD-L1), transforming growth factor beta 1 (TGFB1), and interleukin-10 (IL10) in most cancer types. FUCA2 knockdown inhibited the cell viability in lung cancer cells. Conclusions Our study reveals that FUCA2 is a potential oncogene and is indicative biomarker of a worse prognosis in pan-cancer. High FUCA2 expression may contribute to increased infiltration of TAMs and associates with an immunosuppressive microenvironment, providing a potential target for tumor therapy.
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Affiliation(s)
- Anyuan Zhong
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Ting Chen
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yufei Xing
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xue Pan
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Minhua Shi
- Department of Pulmonary and Critical Care Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
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