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Hong W, Zhang Y, Wang S, Zheng D, Hsu S, Zhou J, Fan J, Zeng Z, Wang N, Ding Z, Yu M, Gao Q, Du S. Deciphering the immune modulation through deep transcriptomic profiling and therapeutic implications of DNA damage repair pattern in hepatocellular carcinoma. Cancer Lett 2024; 582:216594. [PMID: 38135208 DOI: 10.1016/j.canlet.2023.216594] [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: 08/31/2023] [Revised: 11/15/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
AIMS DNA damage repair (DDR) plays a pivotal role in hepatocellular carcinoma (HCC), driving oncogenesis, progression, and therapeutic response. However, the mechanisms of DDR mediated immune cells and immuno-modulatory pathways in HCC are yet ill-defined. METHODS Our study introduces an innovative deep machine learning framework for precise DDR assessment, utilizing single-cell RNA sequencing (scRNA-seq) and bulk RNA-seq data. Single-cell RNA sequencing data were obtained and in total 85,628 cells of primary or post-immunotherapy cases were analyzed. Large-scale HCC datasets, including 1027 patients in house together with public datasets, were used for 101 machine-learning models and a novel DDR feature was derived at single-cell resolution (DDRscore). Druggable targets were predicted using the reverse phase protein array (RPPA) proteomic profiling of 169 HCC patients and RNA-seq data from 22 liver cancer cell lines. RESULTS Our investigation reveals a dynamic interplay of DDR with natural killer cells and B cells in the primary HCC microenvironment, shaping a tumor-promoting immune milieu through metabolic programming. Analysis of HCC post-immunotherapy demonstrates elevated DDR levels that induces epithelial-mesenchymal transition and fibroblast-like transformation, reshaping the fibrotic tumor microenvironment. Conversely, attenuated DDR promotes antigen cross-presentation by dendritic cells and CD8+ T cells, modulating the inflammatory tumor microenvironment. Regulatory network analysis identifies the CXCL10-CXCR3 axis as a key determinant of immunotherapeutic response in low DDR HCC, potentially regulated by transcription factors GATA3, REL, and TBX21. Using machine learning techniques by combining bulk RNA-seq data in house together with public datasets, we introduce DDRscore, a robust consensus DDR scoring system to predict overall survival and resistance to PD-1 therapy in HCC patients. Finally, we identify BRAF as a potential therapeutic target for high DDRscore patients. CONCLUSION Our comprehensive findings advance our understanding of DDR and the tumor microenvironment in HCC, providing insights into immune regulatory mechanisms mediated via DDR pathways.
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Affiliation(s)
- Weifeng Hong
- Department of Radiation Oncology, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200000, China
| | - Yang Zhang
- Department of Radiation Oncology, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200000, China
| | - Siwei Wang
- Department of Radiation Oncology, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200000, China
| | - Danxue Zheng
- Department of Radiation Oncology, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200000, China
| | - Shujung Hsu
- Department of Radiation Oncology, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200000, China
| | - Jian Zhou
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Jia Fan
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Zhaochong Zeng
- Department of Radiation Oncology, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200000, China
| | - Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, Shandong, 250000, China
| | - Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd., Jinan, Shandong, 250000, China
| | - Min Yu
- Department of Pancreas Center, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, 510000, China.
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
| | - Shisuo Du
- Department of Radiation Oncology, Cancer Center, Zhongshan Hospital, Fudan University, Shanghai, 200000, China.
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Salman HR, Al-Zubaidy AA, Abbas AH, Zigam QA. The ameliorative effects of topical gemifloxacin alone or in combination with clobetasol propionate on imiquimod-induced model of psoriasis in mice. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2024; 397:599-616. [PMID: 37490123 DOI: 10.1007/s00210-023-02629-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 07/13/2023] [Indexed: 07/26/2023]
Abstract
Psoriasis is a lifelong immune-driven skin condition characterized by excessive epidermal overgrowth and inflammatory cell infiltration. Gemifloxacin is a fourth-generation fluoroquinolone with improved immunomodulatory and anti-inflammatory properties that are believed to possess an attractive role in psoriasis via suppressing the production of cytokines, chemokines, and eosinophil and neutrophil chemotaxis. The aim of this research is to investigate the ameliorative effects of prolonged topical gemifloxacin (GMF) alone and combined with clobetasol propionate (CLO) on an imiquimod (IMQ)-induced mouse model of psoriasis. Forty-eight Swiss albino mice were divided into six groups of eight. All groups except the negative controls got 62.5 mg of IMQ 5% topically for 8 days. Mice in the control group (controls) got Vaseline instead. Following the induction in the IMQ 5% group, mice in treatment groups CLO 0.05, GMF 1%, GMF 3%, and CLO + GMF obtained clobetasol propionate 0.05%, GMF 1% and 3%, and a combination of both, respectively, for an additional 8 days, rendering the experiment 16 days long. Our results revealed that gemifloxacin alleviated erythematous, thickened, and scaly psoriatic lesions and inhibited the tissue level of inflammatory cytokines, including interleukin (IL)-8, IL-17A, IL-23, tumor necrosis factor-α (TNF-α), and transforming growth factor-β1 (TGF-β1). The anti-inflammatory effect also occurred by hindering nuclear factor-kappa B (NF-κB) signaling and reversing histopathological problems. Gemifloxacin acts effectively in mitigating psoriasis-associated lesions and restricting NF-κB-mediated inflammation, recommending gemifloxacin as a promising adjuvant candidate for additional studies on the long-term treatment of autoimmune and autoinflammatory dermatoses like psoriasis.
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Affiliation(s)
- Hayder Ridha Salman
- Department of Pharmacology, College of Pharmacy, Al-Mustaqbal University, 510001, Hillah, Babylon, Iraq.
- Department of Pharmacology, College of Medicine, Al-Nahrain University, Baghdad, Iraq.
| | - Adeeb Ahmed Al-Zubaidy
- Department of Pharmacology, College of Medicine, University of Warith Al-Anbiyaa, Karbala, Iraq
| | - Alaa Hamza Abbas
- Department of Pharmacology, College of Medicine, Al-Nahrain University, Baghdad, Iraq
| | - Qassim A Zigam
- Department of Pharmacology, College of Pharmacy, Al-Mustaqbal University, 510001, Hillah, Babylon, Iraq
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3
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Todd I, Thomas RE, Watt BD, Sutherland L, Afriyie-Asante A, Deb B, Joseph B, Tighe PJ, Lanyon P, Fairclough LC. Multiple pathways of type 1 interferon production in lupus: the case for amlexanox. Rheumatology (Oxford) 2020; 59:3980-3982. [PMID: 32888016 DOI: 10.1093/rheumatology/keaa469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/04/2020] [Accepted: 06/17/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Ian Todd
- School of Life Sciences, University of Nottingham, Nottingham, UK.,Nottingham Biomedical Research Centre (Musculoskeletal)
| | - Rhema E Thomas
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Baltina D Watt
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Lissa Sutherland
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | | | - Bishnu Deb
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Blessy Joseph
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Patrick J Tighe
- School of Life Sciences, University of Nottingham, Nottingham, UK.,Nottingham Biomedical Research Centre (Musculoskeletal)
| | - Peter Lanyon
- Nottingham Biomedical Research Centre (Musculoskeletal).,Department of Rheumatology, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - Lucy C Fairclough
- School of Life Sciences, University of Nottingham, Nottingham, UK.,Nottingham Biomedical Research Centre (Musculoskeletal)
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4
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Jarosz-Griffiths HH, Holbrook J, Lara-Reyna S, McDermott MF. TNF receptor signalling in autoinflammatory diseases. Int Immunol 2020; 31:639-648. [PMID: 30838383 DOI: 10.1093/intimm/dxz024] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022] Open
Abstract
Autoinflammatory syndromes are a group of disorders characterized by recurring episodes of inflammation as a result of specific defects in the innate immune system. Patients with autoinflammatory disease present with recurrent outbreaks of chronic systemic inflammation that are mediated by innate immune cells, for the most part. A number of these diseases arise from defects in the tumour necrosis factor receptor (TNFR) signalling pathway leading to elevated levels of inflammatory cytokines. Elucidation of the molecular mechanisms of these recently defined autoinflammatory diseases has led to a greater understanding of the mechanisms of action of key molecules involved in TNFR signalling, particularly those involved in ubiquitination, as found in haploinsufficiency of A20 (HA20), otulipenia/OTULIN-related autoinflammatory syndrome (ORAS) and linear ubiquitin chain assembly complex (LUBAC) deficiency. In this review, we also address other TNFR signalling disorders such as TNFR-associated periodic syndrome (TRAPS), RELA haploinsufficiency, RIPK1-associated immunodeficiency and autoinflammation, X-linked ectodermal dysplasia and immunodeficiency (X-EDA-ID) and we review the most recent advances surrounding these diseases and therapeutic approaches currently used to target these diseases. Finally, we explore therapeutic advances in TNF-related immune-based therapies and explore new approaches to target disease-specific modulation of autoinflammatory diseases.
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Affiliation(s)
- Heledd H Jarosz-Griffiths
- Leeds Institute of Rheumatic and Musculoskeletal Medicine (LIRMM), Wellcome Trust Brenner Building, University of Leeds, Leeds, UK.,Leeds Institute of Medical Research at St James's, Clinical Sciences Building, University of Leeds, Leeds, UK.,Leeds Cystic Fibrosis Trust Strategic Research Centre, Wellcome Trust Brenner Building, University of Leeds, Leeds, UK
| | - Jonathan Holbrook
- Leeds Institute of Rheumatic and Musculoskeletal Medicine (LIRMM), Wellcome Trust Brenner Building, University of Leeds, Leeds, UK.,Leeds Institute of Medical Research at St James's, Clinical Sciences Building, University of Leeds, Leeds, UK.,Leeds Cystic Fibrosis Trust Strategic Research Centre, Wellcome Trust Brenner Building, University of Leeds, Leeds, UK
| | - Samuel Lara-Reyna
- Leeds Institute of Rheumatic and Musculoskeletal Medicine (LIRMM), Wellcome Trust Brenner Building, University of Leeds, Leeds, UK.,Leeds Institute of Medical Research at St James's, Clinical Sciences Building, University of Leeds, Leeds, UK.,Leeds Cystic Fibrosis Trust Strategic Research Centre, Wellcome Trust Brenner Building, University of Leeds, Leeds, UK
| | - Michael F McDermott
- Leeds Institute of Rheumatic and Musculoskeletal Medicine (LIRMM), Wellcome Trust Brenner Building, University of Leeds, Leeds, UK.,Leeds Cystic Fibrosis Trust Strategic Research Centre, Wellcome Trust Brenner Building, University of Leeds, Leeds, UK
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Marino A, Tirelli F, Giani T, Cimaz R. Periodic fever syndromes and the autoinflammatory diseases (AIDs). J Transl Autoimmun 2019; 3:100031. [PMID: 32743516 PMCID: PMC7388371 DOI: 10.1016/j.jtauto.2019.100031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 12/13/2019] [Accepted: 12/13/2019] [Indexed: 12/14/2022] Open
Abstract
Innate immune system represents the ancestral defense against infectious agents preserved along the evolution and species; it is phylogenetically older than the adaptive immune system, which exists only in the vertebrates. Cells with phagocytic activity such as neutrophils, macrophages, and natural killer (NK) cells play a key role in innate immunity. In 1999 Kastner et al. first introduced the term “autoinflammation” describing two diseases characterized by recurrent episodes of systemic inflammation without any identifiable infectious trigger: Familial Mediterranean Fever (FMF) and TNF Receptor Associated Periodic Syndrome (TRAPS). Autoinflammatory diseases (AIDs) are caused by self-directed inflammation due to an alteration of innate immunity leading to systemic inflammatory attacks typically in an on/off mode. In addition to inflammasomopathies, nuclear factor (NF)-κB-mediated disorders (also known as Rhelopathies) and type 1 interferonopathies are subjects of more recent studies. This review aims to provide an overview of the field with the most recent updates (see “Most recent developments in..” paragraphs) and a description of the newly identified AIDs. Autoinflammatory diseases are caused by self-directed inflammation. Alteration of innate immunity leads to systemic inflammation attacks. The autoinflammatory field is exponentially expanding. The advances in AIDs have led to new insights into immune system understanding. Autoimmunity and autoinflammation features may be simultaneously present.
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Affiliation(s)
- Achille Marino
- Department of Pediatrics, Desio Hospital, ASST Monza, Desio, MB, Italy.,Biomedical Sciences, University of Florence, Florence, Italy
| | - Francesca Tirelli
- Rheumatology Unit, Meyer Children's Hospital, University of Florence, Florence, Italy
| | - Teresa Giani
- Rheumatology Unit, Meyer Children's Hospital, University of Florence, Florence, Italy.,Department of Medical Biotechnology, University of Siena, Siena, Italy
| | - Rolando Cimaz
- Department of Clinical Sciences and Community Health, University of Milano, Milan, Italy
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6
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Nie X, Wei J, Hao Y, Tao J, Li Y, Liu M, Xu B, Li B. Consistent Biomarkers and Related Pathogenesis Underlying Asthma Revealed by Systems Biology Approach. Int J Mol Sci 2019; 20:ijms20164037. [PMID: 31430856 PMCID: PMC6720652 DOI: 10.3390/ijms20164037] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 08/14/2019] [Accepted: 08/17/2019] [Indexed: 12/13/2022] Open
Abstract
Asthma is a common chronic airway disease worldwide. Due to its clinical and genetic heterogeneity, the cellular and molecular processes in asthma are highly complex and relatively unknown. To discover novel biomarkers and the molecular mechanisms underlying asthma, several studies have been conducted by focusing on gene expression patterns in epithelium through microarray analysis. However, few robust specific biomarkers were identified and some inconsistent results were observed. Therefore, it is imperative to conduct a robust analysis to solve these problems. Herein, an integrated gene expression analysis of ten independent, publicly available microarray data of bronchial epithelial cells from 348 asthmatic patients and 208 healthy controls was performed. As a result, 78 up- and 75 down-regulated genes were identified in bronchial epithelium of asthmatics. Comprehensive functional enrichment and pathway analysis revealed that response to chemical stimulus, extracellular region, pathways in cancer, and arachidonic acid metabolism were the four most significantly enriched terms. In the protein-protein interaction network, three main communities associated with cytoskeleton, response to lipid, and regulation of response to stimulus were established, and the most highly ranked 6 hub genes (up-regulated CD44, KRT6A, CEACAM5, SERPINB2, and down-regulated LTF and MUC5B) were identified and should be considered as new biomarkers. Pathway cross-talk analysis highlights that signaling pathways mediated by IL-4/13 and transcription factor HIF-1α and FOXA1 play crucial roles in the pathogenesis of asthma. Interestingly, three chemicals, polyphenol catechin, antibiotic lomefloxacin, and natural alkaloid boldine, were predicted and may be potential drugs for asthma treatment. Taken together, our findings shed new light on the common molecular pathogenesis mechanisms of asthma and provide theoretical support for further clinical therapeutic studies.
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Affiliation(s)
- Xiner Nie
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Jinyi Wei
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Youjin Hao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Jingxin Tao
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Yinghong Li
- School of Biological Information, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Mingwei Liu
- College of Laboratory Medicine, Chongqing Medical University, Chongqing 400046, China
| | - Boying Xu
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Bo Li
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
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