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Liu C, Zhang Y, Liang Y, Zhang T, Wang G. DrugReSC: targeting disease-critical cell subpopulations with single-cell transcriptomic data for drug repurposing in cancer. Brief Bioinform 2024; 25:bbae490. [PMID: 39350337 PMCID: PMC11442150 DOI: 10.1093/bib/bbae490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/25/2024] [Accepted: 09/17/2024] [Indexed: 10/04/2024] Open
Abstract
The field of computational drug repurposing aims to uncover novel therapeutic applications for existing drugs through high-throughput data analysis. However, there is a scarcity of drug repurposing methods leveraging the cellular-level information provided by single-cell RNA sequencing data. To address this need, we propose DrugReSC, an innovative approach to drug repurposing utilizing single-cell RNA sequencing data, intending to target specific cell subpopulations critical to disease pathology. DrugReSC constructs a drug-by-cell matrix representing the transcriptional relationships between individual cells and drugs and utilizes permutation-based methods to assess drug contributions to cellular phenotypic changes. We demonstrate DrugReSC's superior performance compared to existing drug repurposing methods based on bulk or single-cell RNA sequencing data across multiple cancer case studies. In summary, DrugReSC offers a novel perspective on the utilization of single-cell sequencing data in drug repurposing methods, contributing to the advancement of precision medicine for cancer.
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Affiliation(s)
- Chonghui Liu
- College of Life Science, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, China
- College of Computer and Control Engineering, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Yan Zhang
- Kunming Institute of Zoology, Chinese Academy of Sciences, 17 Longxin Road, Panlong District, Kunming 650201, Yunnan, China
- University of Chinese Academy of Sciences, 1 Yanxi Lake East Road, Huairou District, Beijing 100049, China
| | - Yingjian Liang
- Department of General Surgery, the First Affiliated Hospital of Harbin Medical University, 23 Youzheng Street, Nangang District, Harbin 150007, China
| | - Tianjiao Zhang
- College of Computer and Control Engineering, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, China
| | - Guohua Wang
- College of Computer and Control Engineering, Northeast Forestry University, 26 Hexing Road, Xiangfang District, Harbin 150040, China
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Long Q, Ma T, Wang Y, Chen S, Tang S, Wang T, Zhou Y, Xu K, Wan P, Cao Y. Orientin alleviates the inflammatory response in psoriasis like dermatitis in BALB/c mice by inhibiting the MAPK signaling pathway. Int Immunopharmacol 2024; 134:112261. [PMID: 38761783 DOI: 10.1016/j.intimp.2024.112261] [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: 02/03/2024] [Revised: 05/09/2024] [Accepted: 05/11/2024] [Indexed: 05/20/2024]
Abstract
BACKGROUND Psoriasis, a chronic inflammatory condition of the skin, is characterized by an atypical proliferation of epidermal keratinocytes and immune cell infiltration. Orientin is a flavonoid monomer with potent anti-inflammatory activities. However, the therapeutic effects of orientin on psoriasis and the underlying mechanisms have not been elucidated. OBJECTIVE To investigate the therapeutic effect of orientin on psoriasis and the underlying mechanisms using network pharmacology and experimental studies. METHODS A psoriasis-like mouse model was established using imiquimod (IMQ). Lipopolysaccharide (LPS) was used to stimulate the RAW264.7 and HaCaT cells in vitro. The therapeutic effects of orientin and the underlying mechanism were analyzed using histopathological, immunohistochemical, quantitative real-time polymerase chain reaction, enzyme-linked immunosorbent assay, flow cytometry, and western blotting analyses. RESULTS Orientin ameliorated skin lesions and suppressed keratinocyte proliferation and immune cell infiltration in the IMQ-induced psoriasis-like mouse model. Additionally, orientin inhibited the secretion of the pro-inflammatory factors interleukin (IL)-1β, tumor necrosis factor (TNF)-α, IL-6, IL-8, IL-17, and IL-23 in the psoriasis-like mouse model and LPS-induced RAW264.7 and HaCaT cells. Furthermore, orientin mitigated the LPS-induced upregulation of reactive oxygen species and downregulation of IL-10 and glutathione levels. Orientin alleviated inflammation by downregulating the MAPK signaling pathway. CONCLUSION Orientin alleviated psoriasis-like dermatitis by suppressing the MAPK signaling pathway, suggesting that orientin is a potential therapeutic for psoriasis.
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Affiliation(s)
- Qiu Long
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550000, China; Molecular Biology Laboratory, Guizhou Medical University, Guiyang, Guizhou 550000, China
| | - Ting Ma
- Department of Dermatology, Guizhou Provincial People's Hospital, Guiyang, Guizhou 550000, China
| | - Ye Wang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550000, China
| | - Shaojie Chen
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550000, China; Department of Hepatobiliary Surgery, Guizhou Medical University Hospital, Guiyang, Guizhou 550000, China
| | - Shanshan Tang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550000, China
| | - Tao Wang
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550000, China
| | - Yi Zhou
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550000, China
| | - Kexin Xu
- School of Clinical Medicine, Guizhou Medical University, Guiyang, Guizhou 550000, China
| | - Pengjie Wan
- Department of Dermatology, Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China; Department of Dermatology, Guizhou Branch of Shanghai Children's Medical Center, School of Medicine, Shanghai Jiao Tong University, Guiyang, Guizhou 550000, China.
| | - Yu Cao
- Department of Dermatology, Guizhou Medical University Hospital, Guiyang, Guizhou 550000, China.
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Krueger JG, Eyerich K, Kuchroo VK, Ritchlin CT, Abreu MT, Elloso MM, Fourie A, Fakharzadeh S, Sherlock JP, Yang YW, Cua DJ, McInnes IB. IL-23 past, present, and future: a roadmap to advancing IL-23 science and therapy. Front Immunol 2024; 15:1331217. [PMID: 38686385 PMCID: PMC11056518 DOI: 10.3389/fimmu.2024.1331217] [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: 10/31/2023] [Accepted: 03/21/2024] [Indexed: 05/02/2024] Open
Abstract
Interleukin (IL)-23, an IL-12 cytokine family member, is a hierarchically dominant regulatory cytokine in a cluster of immune-mediated inflammatory diseases (IMIDs), including psoriasis, psoriatic arthritis, and inflammatory bowel disease. We review IL-23 biology, IL-23 signaling in IMIDs, and the effect of IL-23 inhibition in treating these diseases. We propose studies to advance IL-23 biology and unravel differences in response to anti-IL-23 therapy. Experimental evidence generated from these investigations could establish a novel molecular ontology centered around IL-23-driven diseases, improve upon current approaches to treating IMIDs with IL-23 inhibition, and ultimately facilitate optimal identification of patients and, thereby, outcomes.
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Affiliation(s)
- James G. Krueger
- Laboratory for Investigative Dermatology, The Rockefeller University, New York, NY, United States
| | - Kilian Eyerich
- Department of Medicine, Division of Dermatology and Venereology, Karolinska Institute, Stockholm, Sweden
- Department of Dermatology and Venereology, Medical Center, University of Freiburg, Freiburg, Germany
| | - Vijay K. Kuchroo
- Evergrande Center for Immunologic Diseases, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, United States
| | - Christopher T. Ritchlin
- Allergy, Immunology & Rheumatology Division, Center for Musculoskeletal Research, University of Rochester Medical School, Rochester, NY, United States
| | - Maria T. Abreu
- Division of Gastroenterology, Department of Medicine, University of Miami Leonard Miller School of Medicine, Miami, FL, United States
| | | | - Anne Fourie
- Janssen Research & Development, LLC, San Diego, CA, United States
| | - Steven Fakharzadeh
- Immunology Global Medical Affairs, Janssen Pharmaceutical Companies of Johnson & Johnson, Horsham, PA, United States
| | - Jonathan P. Sherlock
- Janssen Research & Development, LLC, Spring House, PA, United States
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Ya-Wen Yang
- Immunology Global Medical Affairs, Janssen Pharmaceutical Companies of Johnson & Johnson, Horsham, PA, United States
| | - Daniel J. Cua
- Janssen Research & Development, LLC, Spring House, PA, United States
| | - Iain B. McInnes
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
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Zhao Q, Wu Y, Wu X, Liu M, Nan L. Single-cell transcriptome analysis reveals keratinocyte subpopulations contributing to psoriasis in corneum and granular layer. Skin Res Technol 2024; 30:e13572. [PMID: 38279596 PMCID: PMC10818132 DOI: 10.1111/srt.13572] [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: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/28/2024]
Abstract
BACKGROUND Psoriasis is a chronic, inflammatory skin disease that is common and relapses easily. While the importance of keratinocyte proliferation in psoriasis development is well-documented, the specific functional subpopulations of epidermal keratinocytes associated with this disease remain enigmatic. MATERIALS AND METHODS Therefore, in our analysis of single-cell transcriptome data from both normal and psoriatic skin tissues, we observed significant increases in certain keratinocytes in the stratum corneum (KC) and stratum granulosum (KG) within psoriatic skin. Furthermore, we identified upregulated expression of specific secreted factors known to promote inflammatory responses. Additionally, we conducted a KEGG pathway enrichment analysis on these identified subsets. RESULTS In the stratum corneum, the expression of FTL was upregulated in HIST1H1C+ KC. S100P+ KC displayed a significant increase in the expression of both S100P and S100A10, whereas PRR9+ KC showed upregulated expression of DEFB4B, S100A8, and S100A12. SLURP1+ KC was characterized by elevated expression levels of IL-36G, SLURP1, and S100A12. Meanwhile, in the stratum granulosum, KRT1+ KG highly expressed SLURP1, S100A7, S100A8, and S100A9, while DEFB4B expression was upregulated in PI3+ KG. Our findings indicated that subsets within the stratum corneum primarily participate in pathways related to MAPK, NOD-like receptors, HIF-1, cell senescence, and other crucial processes. In contrast, subsets in the stratum granulosum were predominantly associated with pathways involving MAPK, NOD-like receptors, HIF-1, Hippo, mTOR, and IL-17. CONCLUSION These findings not only uncover the keratinocyte subsets linked to psoriasis but also unveil the molecular mechanisms and related signaling pathways that drive psoriasis development. This knowledge opens new horizons for the development of innovative clinical treatment strategies for psoriasis.
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Affiliation(s)
- Qianya Zhao
- First Clinical Medical CollegeGansu University of Chinese MedicineLanzhouGansuChina
- Department of DermatologyGansu Provincial HospitalLanzhouGansuChina
| | - Yan Wu
- First Clinical Medical CollegeGansu University of Chinese MedicineLanzhouGansuChina
| | - Xianwei Wu
- First Clinical Medical CollegeGansu University of Chinese MedicineLanzhouGansuChina
- Department of DermatologyGansu Provincial HospitalLanzhouGansuChina
| | - Meng Liu
- First Clinical Medical CollegeGansu University of Chinese MedicineLanzhouGansuChina
- Department of DermatologyGansu Provincial HospitalLanzhouGansuChina
| | - Lisheng Nan
- First Clinical Medical CollegeGansu University of Chinese MedicineLanzhouGansuChina
- Department of DermatologyGansu Provincial HospitalLanzhouGansuChina
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