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Ma X, Zhang Y, Jiang J, Ru Y, Luo Y, Luo Y, Fei X, Song J, Ma X, Li B, Tan Y, Kuai L. Metabolism-related biomarkers, molecular classification, and immune infiltration in diabetic ulcers with validation. Int Wound J 2023; 20:3498-3513. [PMID: 37245869 PMCID: PMC10588317 DOI: 10.1111/iwj.14223] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 04/21/2023] [Indexed: 05/30/2023] Open
Abstract
Diabetes mellitus (DM) can lead to diabetic ulcers (DUs), which are the most severe complications. Due to the need for more accurate patient classifications and diagnostic models, treatment and management strategies for DU patients still need improvement. The difficulty of diabetic wound healing is caused closely related to biological metabolism and immune chemotaxis reaction dysfunction. Therefore, the purpose of our study is to identify metabolic biomarkers in patients with DU and construct a molecular subtype-specific prognostic model that is highly accurate and robust. RNA-sequencing data for DU samples were obtained from the Gene Expression Omnibus (GEO) database. DU patients and normal individuals were compared regarding the expression of metabolism-related genes (MRGs). Then, a novel diagnostic model based on MRGs was constructed with the random forest algorithm, and classification performance was evaluated utilizing receiver operating characteristic (ROC) analysis. The biological functions of MRGs-based subtypes were investigated using consensus clustering analysis. A principal component analysis (PCA) was conducted to determine whether MRGs could distinguish between subtypes. We also examined the correlation between MRGs and immune infiltration. Lastly, qRT-PCR was utilized to validate the expression of the hub MRGs with clinical validations and animal experimentations. Firstly, 8 metabolism-related hub genes were obtained by random forest algorithm, which could distinguish the DUs from normal samples validated by the ROC curves. Secondly, DU samples could be consensus clustered into three molecular classifications by MRGs, verified by PCA analysis. Thirdly, associations between MRGs and immune infiltration were confirmed, with LYN and Type 1 helper cell significantly positively correlated; RHOH and TGF-β family remarkably negatively correlated. Finally, clinical validations and animal experiments of DU skin tissue samples showed that the expressions of metabolic hub genes in the DU groups were considerably upregulated, including GLDC, GALNT6, RHOH, XDH, MMP12, KLK6, LYN, and CFB. The current study proposed an auxiliary MRGs-based DUs model while proposing MRGs-based molecular clustering and confirmed the association with immune infiltration, facilitating the diagnosis and management of DU patients and designing individualized treatment plans.
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Affiliation(s)
- Xiao‐Xuan Ma
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina
- Institute of DermatologyShanghai Academy of Traditional Chinese MedicineshanghaiChina
| | - Ying Zhang
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina
- Institute of DermatologyShanghai Academy of Traditional Chinese MedicineshanghaiChina
| | - Jing‐Si Jiang
- Shanghai Skin Disease Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Yi Ru
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina
- Institute of DermatologyShanghai Academy of Traditional Chinese MedicineshanghaiChina
| | - Ying Luo
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina
- Institute of DermatologyShanghai Academy of Traditional Chinese MedicineshanghaiChina
| | - Yue Luo
- Shanghai Skin Disease Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Xiao‐Ya Fei
- Shanghai Skin Disease Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Jian‐Kun Song
- Shanghai Skin Disease Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Xin Ma
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina
- Institute of DermatologyShanghai Academy of Traditional Chinese MedicineshanghaiChina
- Shanghai Skin Disease Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Bin Li
- Institute of DermatologyShanghai Academy of Traditional Chinese MedicineshanghaiChina
- Shanghai Skin Disease Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Yi‐Mei Tan
- Shanghai Skin Disease Hospital, School of MedicineTongji UniversityShanghaiChina
| | - Le Kuai
- Department of Dermatology, Yueyang Hospital of Integrated Traditional Chinese and Western MedicineShanghai University of Traditional Chinese MedicineShanghaiChina
- Institute of DermatologyShanghai Academy of Traditional Chinese MedicineshanghaiChina
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Milewska A, Falkowski K, Kulczycka M, Bielecka E, Naskalska A, Mak P, Lesner A, Ochman M, Urlik M, Diamandis E, Prassas I, Potempa J, Kantyka T, Pyrc K. Kallikrein 13 serves as a priming protease during infection by the human coronavirus HKU1. Sci Signal 2020; 13:13/659/eaba9902. [PMID: 33234691 PMCID: PMC7857416 DOI: 10.1126/scisignal.aba9902] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Unlike SARS-CoV-2, the human coronavirus HKU1 normally causes relatively mild respiratory tract infections; however, it shares with SARS-CoV-2 the mechanism of using its surface spike (S) protein to enter target cells. Because the host receptor for HCoV-HKU1 is unknown, efforts to study the virus in cell culture systems have proved difficult. Milewska et al. found that knockout of the protease kallikrein 13 (KLK13) in human airway epithelial cells blocked their infection by HCoV-HKU1, that overexpression of KLK13 in nonpermissive cells enabled their infection by the virus, and that KLK13 cleaved the viral S protein. Together, these findings suggest that KLK13 is a priming enzyme for viral entry and may help to establish cell lines that can facilitate further investigation of the mechanism of viral pathogenesis. Human coronavirus HKU1 (HCoV-HKU1) is associated with respiratory disease and is prevalent worldwide, but an in vitro model for viral replication is lacking. An interaction between the coronaviral spike (S) protein and its receptor is the primary determinant of tissue and host specificity; however, viral entry is a complex process requiring the concerted action of multiple cellular elements. Here, we found that the protease kallikrein 13 (KLK13) was required for the infection of human respiratory epithelial cells and was sufficient to mediate the entry of HCoV-HKU1 into nonpermissive RD cells. We also demonstrated the cleavage of the HCoV-HKU1 S protein by KLK13 in the S1/S2 region, suggesting that KLK13 is the priming enzyme for this virus. Together, these data suggest that protease distribution and specificity determine the tissue and cell specificity of the virus and may also regulate interspecies transmission.
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Affiliation(s)
- Aleksandra Milewska
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.,Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Katherine Falkowski
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Magdalena Kulczycka
- Laboratory of Proteolysis and Post-translational Modification of Proteins, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Ewa Bielecka
- Laboratory of Proteolysis and Post-translational Modification of Proteins, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland
| | - Antonina Naskalska
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland
| | - Pawel Mak
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7 St., 30-387 Krakow, Poland
| | - Adam Lesner
- Faculty of Chemistry, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland
| | - Marek Ochman
- Department of Cardiac, Vascular and Endovascular Surgery and Transplantology, Medical University of Silesia in Katowice, Silesian Centre for Heart Diseases, Zabrze, Poland
| | - Maciej Urlik
- Department of Cardiac, Vascular and Endovascular Surgery and Transplantology, Medical University of Silesia in Katowice, Silesian Centre for Heart Diseases, Zabrze, Poland
| | - Elftherios Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada.,Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada.,Department of Clinical Biochemistry, University Health Network, Toronto, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Ioannis Prassas
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Canada.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Jan Potempa
- Microbiology Department, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.,Centre for Oral Health and Systemic Diseases, University of Louisville School of Dentistry, Louisville, KY 40202, USA
| | - Tomasz Kantyka
- Laboratory of Proteolysis and Post-translational Modification of Proteins, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.,Broegelmann Research Laboratory, Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
| | - Krzysztof Pyrc
- Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland.
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Kallikreins - The melting pot of activity and function. Biochimie 2015; 122:270-82. [PMID: 26408415 DOI: 10.1016/j.biochi.2015.09.023] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 09/21/2015] [Indexed: 12/20/2022]
Abstract
The human tissue kallikrein and kallikrein-related peptidases (KLKs), encoded by the largest contiguous cluster of protease genes in the human genome, are secreted serine proteases with diverse expression patterns and physiological roles. Because of the broad spectrum of processes that are modulated by kallikreins, these proteases are the subject of extensive investigations. This review brings together basic information about the biochemical properties affecting enzymatic activity, with highlights on post-translational modifications, especially glycosylation. Additionally, we present the current state of knowledge regarding the physiological functions of KLKs in major human organs and outline recent discoveries pertinent to the involvement of kallikreins in cell signaling and in viral infections. Despite the current depth of knowledge of these enzymes, many questions regarding the roles of kallikreins in health and disease remain unanswered.
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