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Zhou S, Hu J, Du S, Wang F, Fang Y, Zhang R, Wang Y, Zheng L, Gao M, Tang H. RNA-binding proteins potentially regulate alternative splicing of immune/inflammatory-associated genes during the progression of generalized pustular psoriasis. Arch Dermatol Res 2024; 316:538. [PMID: 39158708 DOI: 10.1007/s00403-024-03283-8] [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: 07/09/2024] [Revised: 07/09/2024] [Accepted: 08/05/2024] [Indexed: 08/20/2024]
Abstract
Generalized pustular psoriasis (GPP) is a rare but severe form of psoriasis. However, the pathogenesis of GPP has not been fully elucidated. Although RNA-binding proteins (RBPs) and the alternative splicing (AS) process are essential for regulating post-transcriptional gene expression, their roles in GPP are still unclear. We aimed to elucidate the regulatory mechanisms to identify potential new therapeutic targets. Here, We analyzed an RNA sequencing (RNA-seq) dataset (GSE200977) of peripheral blood mononuclear cells (PBMCs) of 24 patients with GPP, psoriasis vulgaris (PV), and healthy controls (HCs) from the Gene Expression Omnibus (GEO) database. We found that the abnormal alternative splicing (AS) events associated with GPP were mainly "alt3p/alt5p", and 15 AS genes were differentially expressed. Notably, the proportions of different immune cell types were correlated with the expression levels of regulatory alternatively spliced genes (RASGs): significant differences were observed in expression levels of DTD2, NDUFAF3, NBPF15, and FBLN7 in B cells and ARFIP1, IPO11, and RP11-326L24.9 in neutrophils in the GPP samples. Furthermore, We identified 32 differentially expressed RNA-binding proteins (RBPs) (18 up-regulated and 14 down-regulated). Co-expression networks between 14 pairs of differentially expressed RBPs and RASGs were subsequently constructed, demonstrating that these differentially expressed RBPs may affect the progression of GPP by regulating the AS of downstream immune/inflammatory-related genes such as LINC00989, ENC1 and MMP25-AS1. Our results were innovative in revealing the involvement of inflammation-related RBPs and RASGs in the development of GPP from the perspective of RBP-regulated AS.
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Affiliation(s)
- Shan Zhou
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, Anhui, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Junjie Hu
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, Anhui, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Shuli Du
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, Anhui, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Fang Wang
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, Anhui, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Ying Fang
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, Anhui, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Ranran Zhang
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, Anhui, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Yixiao Wang
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, Anhui, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Liyun Zheng
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China
- Institute of Dermatology, Anhui Medical University, Hefei, 230032, Anhui, China
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, Anhui, China
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Min Gao
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China.
- Institute of Dermatology, Anhui Medical University, Hefei, 230032, Anhui, China.
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, Anhui, China.
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, 230032, Anhui, China.
| | - Huayang Tang
- Department of Dermatology, The First Affiliated Hospital, Anhui Medical University, Hefei, 230032, Anhui, China.
- Institute of Dermatology, Anhui Medical University, Hefei, 230032, Anhui, China.
- Key Laboratory of Dermatology (Anhui Medical University), Ministry of Education, Hefei, 230032, Anhui, China.
- Collaborative Innovation Center of Complex and Severe Skin Disease, Anhui Medical University, Hefei, 230032, Anhui, China.
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Benmelech S, Le T, McKay M, Nam J, Subramaniam K, Tellez D, Vlasak G, Mak M. Biophysical and biochemical aspects of immune cell-tumor microenvironment interactions. APL Bioeng 2024; 8:021502. [PMID: 38572312 PMCID: PMC10990568 DOI: 10.1063/5.0195244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/19/2024] [Indexed: 04/05/2024] Open
Abstract
The tumor microenvironment (TME), composed of and influenced by a heterogeneous set of cancer cells and an extracellular matrix, plays a crucial role in cancer progression. The biophysical aspects of the TME (namely, its architecture and mechanics) regulate interactions and spatial distributions of cancer cells and immune cells. In this review, we discuss the factors of the TME-notably, the extracellular matrix, as well as tumor and stromal cells-that contribute to a pro-tumor, immunosuppressive response. We then discuss the ways in which cells of the innate and adaptive immune systems respond to tumors from both biochemical and biophysical perspectives, with increased focus on CD8+ and CD4+ T cells. Building upon this information, we turn to immune-based antitumor interventions-specifically, recent biophysical breakthroughs aimed at improving CAR-T cell therapy.
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Affiliation(s)
- Shoham Benmelech
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Thien Le
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Maggie McKay
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Jungmin Nam
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Krupakar Subramaniam
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06511, USA
| | - Daniela Tellez
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Grace Vlasak
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA
| | - Michael Mak
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut 06511, USA
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Tan S, Pan S, Wei L, Chen W, Pan B, Kong G, Chen J, Xie Y. Association of peripheral B cells and delirium: combined single-cell sequencing and Mendelian randomization analysis. Front Neurol 2024; 15:1343726. [PMID: 38379709 PMCID: PMC10876872 DOI: 10.3389/fneur.2024.1343726] [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: 11/24/2023] [Accepted: 01/23/2024] [Indexed: 02/22/2024] Open
Abstract
Background Delirium seriously affects the prognosis of patients and greatly reduces the ability to work and live. Peripheral inflammatory events may contribute to the development of delirium, the mechanism of which is still unclear. There is a lack of effective diagnostic and treatments for delirium in clinical practice. The study aims to investigate alterations in peripheral immune cell subsets under inflammatory stress and to explore causal associations with delirium. Methods Single-cell transcriptional sequencing data of human peripheral blood mononuclear cells (PBMC) before and after lipopolysaccharide (LPS) intervention were processed by the Seurat package in R software. PBMC subsets and cellular markers were defined after downscaling and clustering by the Harmony algorithm to identify characteristic subsets in the context of inflammatory stress. Subsequently, a two-sample Mendelian randomization (MR) study was used to explore the causal associations of these inflammation-related PBMC subsets and their molecular phenotypes with delirium. Based on publicly available genetic data, the study incorporated 70 PBMC-associated immune traits, including 8 types of circulating immune cells, 33 B cell subsets and molecular phenotypes, 13 T cell subsets, and 16 B cell-associated cytokines. The results were also validated for robustness, heterogeneity, and horizontal pleiotropy. Results Under LPS-induced inflammatory stress, B cells, T cells, monocytes, and dendritic cells in human PBMC showed significant activation and quantitative changes. Of these, only lymphocyte and B cell counts were causally associated with delirium risk. This risk link is also seen in the TNF pathway. Further studies of B cells and their subsets revealed that this association may be related to unswitched memory B cells and CD27 expressed on memory B cells. Annotation of the screened SNPs revealed significant polymorphisms in CD27 and CD40 annotated by rs25680 and rs9883798, respectively. The functions of the key annotated genes may be related to the regulation of immune responses, cell differentiation, proliferation, and intercellular interactions. Conclusion The present study revealed the potential possibility that B cell, memory B cell subset, and TNF-related molecules may be involved in the development of delirium due to peripheral inflammation, which can provide clues for further investigation of delirium prevention and treatment strategies.
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Affiliation(s)
- Siyou Tan
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Sining Pan
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Lai Wei
- Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Wenyan Chen
- Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Bingbing Pan
- Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Gaoyin Kong
- Department of Anesthesiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Changsha, China
| | - Jing Chen
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yubo Xie
- Department of Anesthesiology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
- Guangxi Key Laboratory of Enhanced Recovery After Surgery for Gastrointestinal Cancer, The First Affiliated Hospital of Guangxi Medical University, Nanning, China
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Li H, Lin WP, Zhang ZN, Sun ZJ. Tailoring biomaterials for monitoring and evoking tertiary lymphoid structures. Acta Biomater 2023; 172:1-15. [PMID: 37739247 DOI: 10.1016/j.actbio.2023.09.028] [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: 07/11/2023] [Revised: 09/01/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023]
Abstract
Despite the remarkable clinical success of immune checkpoint blockade (ICB) in the treatment of cancer, the response rate to ICB therapy remains suboptimal. Recent studies have strongly demonstrated that intratumoral tertiary lymphoid structures (TLSs) are associated with a good prognosis and a successful clinical response to immunotherapy. However, there is still a shortage of efficient and wieldy approaches to image and induce intratumoral TLSs in vivo. Biomaterials have made great strides in overcoming the deficiencies of conventional diagnosis and therapies for cancer, and antitumor therapy has also benefited from biomaterial-based drug delivery models. In this review, we summarize the reported methods for TLS imaging and induction based on biomaterials and provide potential strategies that can further enhance the effectiveness of imaging and stimulating intratumoral TLSs to predict and promote the response rates of ICB therapies for patients. STATEMENT OF SIGNIFICANCE: In this review, we focused on the promising of biomaterials for imaging and induction of TLSs. We reviewed the applications of biomaterials in molecular imaging and immunotherapy, identified the biomaterials that may be suitable for TLS imaging and induction, and provided outlooks for further research. Accurate imaging and effective induction of TLSs are of great significance for understanding the mechanism and clinical application. We highlighted the need for multidisciplinary coordination and cooperation in this field, and proposed the possible future direction of noninvasive imaging and artificial induction of TLSs based on biomaterials. We believe that it can facilitate collaboration and galvanize a broader effort.
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Affiliation(s)
- Hao Li
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430079, PR China; Department of Oral Maxillofacial-Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, PR China
| | - Wen-Ping Lin
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430079, PR China
| | - Zhong-Ni Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430079, PR China
| | - Zhi-Jun Sun
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan 430079, PR China; Department of Oral Maxillofacial-Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan 430079, PR China.
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Liu S, Wang H, Shao X, Chen H, Chao S, Zhang Y, Gao Z, Yao Q, Zhang P. Advances in PD-1 signaling inhibition-based nano-delivery systems for tumor therapy. J Nanobiotechnology 2023; 21:207. [PMID: 37403095 PMCID: PMC10318732 DOI: 10.1186/s12951-023-01966-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023] Open
Abstract
In recent years, cancer immunotherapy has emerged as an exciting cancer treatment. Immune checkpoint blockade brings new opportunities for more researchers and clinicians. Programmed cell death receptor-1 (PD-1) is a widely studied immune checkpoint, and PD-1 blockade therapy has shown promising results in a variety of tumors, including melanoma, non-small cell lung cancer and renal cell carcinoma, which greatly improves patient overall survival and becomes a promising tool for the eradication of metastatic or inoperable tumors. However, low responsiveness and immune-related adverse effects currently limit its clinical application. Overcoming these difficulties is a major challenge to improve PD-1 blockade therapies. Nanomaterials have unique properties that enable targeted drug delivery, combination therapy through multidrug co-delivery strategies, and controlled drug release through sensitive bonds construction. In recent years, combining nanomaterials with PD-1 blockade therapy to construct novel single-drug-based or combination therapy-based nano-delivery systems has become an effective mean to address the limitations of PD-1 blockade therapy. In this study, the application of nanomaterial carriers in individual delivery of PD-1 inhibitors, combined delivery of PD-1 inhibitors and other immunomodulators, chemotherapeutic drugs, photothermal reagents were reviewed, which provides effective references for designing new PD-1 blockade therapeutic strategies.
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Affiliation(s)
- Songlin Liu
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery System, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117, Shandong, China
| | - Haiyang Wang
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery System, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117, Shandong, China
- Qingdao University of Science and Technology, Qingdao, 266042, People's Republic of China
| | - Xinzhe Shao
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery System, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117, Shandong, China
| | - Haonan Chen
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery System, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117, Shandong, China
| | - Shushu Chao
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery System, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117, Shandong, China
| | - Yanyan Zhang
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery System, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117, Shandong, China
| | - Zhaoju Gao
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery System, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117, Shandong, China
| | - Qingqiang Yao
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery System, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117, Shandong, China
| | - Pingping Zhang
- School of Pharmaceutical Sciences & Institute of Materia Medica, Shandong First Medical University & Shandong Academy of Medical Sciences, National Key Laboratory of Advanced Drug Delivery System, Key Laboratory for Biotechnology Drugs of National Health Commission (Shandong Academy of Medical Sciences), Key Lab for Rare & Uncommon Diseases of Shandong Province, Jinan, 250117, Shandong, China.
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Shakiba D, Genin GM, Zustiak SP. Mechanobiology of cancer cell responsiveness to chemotherapy and immunotherapy: Mechanistic insights and biomaterial platforms. Adv Drug Deliv Rev 2023; 196:114771. [PMID: 36889646 PMCID: PMC10133187 DOI: 10.1016/j.addr.2023.114771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/17/2022] [Accepted: 03/03/2023] [Indexed: 03/08/2023]
Abstract
Mechanical forces are central to how cancer treatments such as chemotherapeutics and immunotherapies interact with cells and tissues. At the simplest level, electrostatic forces underlie the binding events that are critical to therapeutic function. However, a growing body of literature points to mechanical factors that also affect whether a drug or an immune cell can reach a target, and to interactions between a cell and its environment affecting therapeutic efficacy. These factors affect cell processes ranging from cytoskeletal and extracellular matrix remodeling to transduction of signals by the nucleus to metastasis of cells. This review presents and critiques the state of the art of our understanding of how mechanobiology impacts drug and immunotherapy resistance and responsiveness, and of the in vitro systems that have been of value in the discovery of these effects.
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Affiliation(s)
- Delaram Shakiba
- NSF Science and Technology Center for Engineering Mechanobiology, Washington University, St. Louis, MO, USA; Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, MO, USA
| | - Guy M Genin
- NSF Science and Technology Center for Engineering Mechanobiology, Washington University, St. Louis, MO, USA; Department of Mechanical Engineering and Materials Science, Washington University, St. Louis, MO, USA.
| | - Silviya P Zustiak
- NSF Science and Technology Center for Engineering Mechanobiology, Washington University, St. Louis, MO, USA; Department of Biomedical Engineering, School of Science and Engineering, Saint Louis University, St. Louis, MO, USA.
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Luo L, Li A, Fu S, Du W, He LN, Zhang X, Wang Y, Zhou Y, Yunpeng Y, Li Z, Hong S. [Cuproptosis-related immune gene signature predicts clinical benefits from anti-PD-1/PD-L1 therapy in non-small-cell lung cancer. Immunol Res 2022; 71:213-228. [PMID: 36434349 DOI: 10.1007/s12026-022-09335-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/24/2022] [Indexed: 11/26/2022]
Abstract
Non-small-cell lung cancer (NSCLC) remains the major cause of cancer-related death. Immune checkpoint inhibition has become the cornerstone treatment for NSCLC. Cuproptosis is a newly identified form of cell death relying on mitochondrial respiration that might play a role in shaping tumor immune microenvironment (TIME). The clinical significance of cuproptosis-related genes (CRGs) remains unclear and warrant investigation. The current study extracted RNA sequencing profiles and corresponding clinical information from six aggregated datasets from the Gene Expression Omnibus (GEO) repository as the training set, and from The Cancer Genome Atlas (TCGA) database as the testing set. Cuproptosis-related immune genes (CRIMGs) were obtained through coexpression analysis, univariate Cox regression analysis, and LASSO analysis for overall survival (OS) association analysis. Consensus clustering was employed to divide the subjects into clusters. Stepwise multivariate Cox regression was used to establish the prognostic CRIMG_score from the CRIMGs. A 17-gene prediction signature was established that informed patients' OS both in the training and testing datasets (p < 0.001). The predictive value of the signature in terms of immunotherapeutic responses was assessed in two publicly available NSCLC immunotherapy datasets (POPLAR and OAK studies) and an internal dataset from Sun Yat-sen University Cancer Center (ORIENT-11 study). Patients in the high-risk group displayed worse survival, a characteristic suppressive tumor immune microenvironment, and low immunotherapeutic benefits compared to those in the low-risk group. Collectively, the CRIMG_score established herein could serve as a promising indicator of prognosis and immunotherapeutic response in patients with NSCLC.
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Effect of Tertiary Lymphoid Structures on Prognosis of Patients with Hepatocellular Carcinoma and Preliminary Exploration of Its Formation Mechanism. Cancers (Basel) 2022; 14:cancers14205157. [PMID: 36291944 PMCID: PMC9601110 DOI: 10.3390/cancers14205157] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/07/2022] [Accepted: 10/13/2022] [Indexed: 11/18/2022] Open
Abstract
Simple Summary At present, research on tertiary lymphoid structures (TLSs) in hepatocellular carcinoma (HCC) has been limited to the prognostic impact. Our manuscript first validates previous studies using two databases and then initially explores the key molecules and mechanisms of TLS formation and immunotherapy implications for HCC patients by using the TCGA database. For example, LCK, a key molecule in the formation of TLSs, may affect the formation of TLSs by regulating the cytokine signalling pathway, chemokine signalling pathway, T-cell activation and P53 signalling pathway. Second, the expression level of LCK is another factor affecting the sensitivity of HCC patients to immune checkpoint inhibitors. In conclusion, our study provides a potential mechanism for further exploration of TLSs. Abstract Background: Tertiary lymphoid structures (TLSs) are formed by the aggregation of tumour-infiltrating lymphocytes (TILs), which is driven by chemokines or cytokines in the tumour microenvironment. Studies have shown that TLSs are associated with good prognosis in patients with various solid tumours and can improve patient responses to immunotherapy. However, the role of TLSs in hepatocellular carcinoma (HCC) remains controversial, and the underlying molecular mechanism is unclear. Methods: According to haematoxylin-eosin (HE) staining results, HCC patients in Xijing Hospital data and TCGA data were divided into TLS+ and TLS- groups, and Kaplan–Meier (KM) analysis was performed to assess overall survival (OS) and recurrence-free survival (RFS). Immunofluorescence (IF) and immunohistochemistry (IHC) were used to identify TILs in the TLS+ group. Lymphocyte-specific protein tyrosine kinase (LCK), a molecule involved in TLS formation, was explored in LinkedOmics. TILs were divided into two groups by drawing receiver operating characteristic (ROC) curves to calculate cut-off values. Spearman correlation analysis was used to calculate the correlation between LCK and TILs, and the molecular pathways by which LCK regulates immunotherapy were clarified through enrichment analysis. The half-maximal inhibitory concentration (IC50) distribution of sorafenib was observed in groups that varied in LCK expression. Results: According to the HE results, 61 cases in the Xijing Hospital cohort and 195 cases in the TCGA cohort had TLSs, while 89 cases and 136 cases did not. The KM results showed that TLSs had no effect on the OS of HCC patients but significantly affected RFS. The IF/IHC results showed that higher TIL numbers in TLSs were correlated with better prognosis in HCC patients. Spearman correlation analysis showed that LCK expression was positively correlated with TIL numbers. Enrichment analysis showed that upregulation of LCK expression mainly regulated the cytokine signalling pathway, the chemokine signalling pathway and T-cell activation. The IC50 scores of sorafenib in HCC patients with high LCK expression were lower, and the sensitivity was higher. Conclusion: TLSs mainly affected the early RFS of HCC patients but had no effect on OS. The high expression of the TLS formation-related gene LCK can increase the sensitivity of HCC patients to ICIs.
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Simsek H, Klotzsch E. The solid tumor microenvironment-Breaking the barrier for T cells: How the solid tumor microenvironment influences T cells: How the solid tumor microenvironment influences T cells. Bioessays 2022; 44:e2100285. [PMID: 35393714 DOI: 10.1002/bies.202100285] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 12/20/2022]
Abstract
The tumor microenvironment (TME) plays a pivotal role in the behavior and development of solid tumors as well as shaping the immune response against them. As the tumor cells proliferate, the space they occupy and their physical interactions with the surrounding tissue increases. The growing tumor tissue becomes a complex dynamic structure, containing connective tissue, vascular structures, and extracellular matrix (ECM) that facilitates stimulation, oxygenation, and nutrition, necessary for its fast growth. Mechanical cues such as stiffness, solid stress, interstitial fluid pressure (IFP), matrix density, and microarchitecture influence cellular functions and ultimately tumor progression and metastasis. In this fight, our body is equipped with T cells as its spearhead against tumors. However, the altered biochemical and mechanical environment of the tumor niche affects T cell efficacy and leads to their exhaustion. Understanding the mechanobiological properties of the TME and their effects on T cells is key for developing novel adoptive tumor immunotherapies.
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Affiliation(s)
- Hasan Simsek
- Institute for Biology, Experimental Biophysics/Mechanobiology, Humboldt University of Berlin, Berlin, Germany
| | - Enrico Klotzsch
- Institute for Biology, Experimental Biophysics/Mechanobiology, Humboldt University of Berlin, Berlin, Germany.,Laboratory of Applied Mechanobiology, Department for Health Sciences and Technology, ETH Zürich, Zürich, Switzerland
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Special Issue: Immunomodulatory Biomaterials. Acta Biomater 2021; 133:1-3. [PMID: 34610878 DOI: 10.1016/j.actbio.2021.09.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Benvenuto M, Focaccetti C, Ciuffa S, Fazi S, Bei A, Miele MT, Albonici L, Cifaldi L, Masuelli L, Bei R. Polyphenols affect the humoral response in cancer, infectious and allergic diseases and autoimmunity by modulating the activity of T H1 and T H2 cells. Curr Opin Pharmacol 2021; 60:315-330. [PMID: 34520942 DOI: 10.1016/j.coph.2021.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/25/2022]
Abstract
Polyphenols are a wide class of natural substances, pleiotropic molecules capable of modulating several processes, involved in the humoral and cellular immune response. The activation, differentiation of B cells, and production of antibodies to protein antigens by plasma cells depend on T helper (TH) CD4+ cells and secreted cytokines. Cancer, infectious, allergic, and autoimmune diseases are characterized by an imbalance of TH1/TH2 immunity and abnormal activation of the humoral response. Accordingly, polyphenols modulate the TH1/TH2 ratio, the secretion of multiple cytokines, the levels of antibodies, and therefore could contribute to recovering the state of health in these diseases. In this review, we summarize the current knowledge on the effects of polyphenols in modulating the humoral response in cancer, infectious and allergic diseases and in autoimmunity by affecting the activity of TH1 and TH2 cells.
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Affiliation(s)
- Monica Benvenuto
- Saint Camillus International University of Health and Medical Sciences, Via di Sant'Alessandro 8, 00131 Rome, Italy; Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Chiara Focaccetti
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy; Department of Human Science and Promotion of the Quality of Life, San Raffaele University Rome, Via di Val Cannuta 247, 00166 Rome, Italy
| | - Sara Ciuffa
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Sara Fazi
- Department of Experimental Medicine, University of Rome "Sapienza", Viale Regina Elena 324, 00161 Rome, Italy
| | - Arianna Bei
- Medical School, University of Rome "Tor Vergata", 00133 Rome, Italy
| | - Martino Tony Miele
- Department of Experimental Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Loredana Albonici
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy
| | - Loredana Cifaldi
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy; Academic Department of Pediatrics (DPUO), Ospedale Pediatrico Bambino Gesù, IRCCS, Piazza Sant'Onofrio 4, 00165 Rome, Italy
| | - Laura Masuelli
- Department of Experimental Medicine, University of Rome "Sapienza", Viale Regina Elena 324, 00161 Rome, Italy
| | - Roberto Bei
- Department of Clinical Sciences and Translational Medicine, University of Rome "Tor Vergata", Via Montpellier 1, 00133 Rome, Italy.
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Xie Z, Li M, Hong H, Xu Q, He Z, Peng Z. Expression of N 6-methyladenosine (m 6A) regulators correlates with immune microenvironment characteristics and predicts prognosis in diffuse large cell lymphoma (DLBCL). Bioengineered 2021; 12:6115-6133. [PMID: 34482808 PMCID: PMC8806613 DOI: 10.1080/21655979.2021.1972644] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
This study conducted a comprehensive analysis of the clinical significance of N6-methyladenosine (m6A) regulators and their relationship with immune microenvironment characteristics in diffuse large cell lymphoma (DLBCL). Consensus clustering was performed to molecularly discriminate DLBCL subtypesbased on m6A regulators’ expression. Using the Cox and Lasso regression algorithm, survival-associated m6A regulators were identified, and a m6A-based prognostic signature was established. The influence of m6A risk on immune cell infiltration, immune checkpoint genes, cancer immunity cycle, and immunotherapeutic response was evaluated. Potential molecular pathways related to m6A risk were investigated using gene set enrichment analysis. The m6A regulators showed satisfactory performance in distinguishing DLBCL subgroups with distinct clinical traits and outcomes. A six m6A regulator-based prognostic signature was established and validated as an independent predictor, which separated patients into low- and high-risk groups. High-risk m6A indicated worse survival. The B cells naïve, T cells gamma delta, and NK cells resting were the three most affected immune cells by m6A risk. Up-regulated (PDCD1 and KIR3DL1) and down-regulated (TIGIT, IDO1, and BTLA) immune checkpoint genes in the high-risk group were identified. The m6A risk was found to influence several steps in the cancer immunity cycle. Patients with high-risk m6A were more likely to benefit from immunotherapy. Biological function enrichment analysis revealed that high-risk m6A to be tended related to malignant tumor characteristics, while low-risk m6A showed trend to be related to defensive response processes. Collectively, the m6A-based prognostic signature could be a practical prognostic predictor for DLBCL and immune microenvironment characteristics affected by m6A may be part of the mechanism.
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Affiliation(s)
- Zucheng Xie
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Meiwei Li
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Haoyuan Hong
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Qingyuan Xu
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Zhendong He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
| | - Zhigang Peng
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region, P. R. China
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Wu G, Yan Y, Cai Y, Peng B, Li J, Huang J, Xu Z, Zhou J. ALKBH1-8 and FTO: Potential Therapeutic Targets and Prognostic Biomarkers in Lung Adenocarcinoma Pathogenesis. Front Cell Dev Biol 2021; 9:633927. [PMID: 34150745 PMCID: PMC8209387 DOI: 10.3389/fcell.2021.633927] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 05/03/2021] [Indexed: 02/05/2023] Open
Abstract
The AlkB family consists of Fe(II)- and α-ketoglutarate-dependent dioxygenases that can catalyze demethylation on a variety of substrates, such as RNA and DNA, subsequently affecting tumor progression and prognosis. However, their detailed functional roles in lung adenocarcinoma (LUAD) have not been clarified in a comprehensive manner. In this study, several bioinformatics databases, such as ONCOMINE, TIMER, and DiseaseMeth, were used to evaluate the expression profiles and prognostic significance of the AlkB family (ALKBH1-8 and FTO) in LUAD. The expression levels of ALKBH1/2/4/5/7/8 were significantly increased in LUAD tissues, while the expression levels of ALKBH3/6 and FTO were decreased. The main functions of differentially expressed AlkB homologs are related to the hematopoietic system and cell adhesion molecules. We also found that the expression profiles of the AlkB family are highly correlated with infiltrating immune cells (i.e., B cells, CD8 + T cells, CD4 + T cells, macrophages, neutrophils and dendritic cells). In addition, DNA methylation analysis indicated that the global methylation levels of ALKBH1/2/4/5/6/8 and FTO were decreased, while the global methylation levels of ALKBH3/7 were increased. In addition, the patients with upregulated ALKBH2 have significantly poor overall survival (OS) and post-progressive survival (PPS). Taken together, our work could provide insightful information about aberrant AlkB family members as potential biomarkers for the diagnostic and prognostic evaluation of LUAD. Especially, ALKBH2 could be served as a therapeutic candidate for treating LUAD.
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Affiliation(s)
- Geting Wu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Yuanliang Yan
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Cai
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Bi Peng
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Juanni Li
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
| | - Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN, United States
| | - Zhijie Xu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Jianhua Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, China
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