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Luo Y, Zhou LQ, Yang F, Chen JC, Chen JJ, Wang YJ. Construction and analysis of a conjunctive diagnostic model of HNSCC with random forest and artificial neural network. Sci Rep 2023; 13:6736. [PMID: 37185487 PMCID: PMC10130066 DOI: 10.1038/s41598-023-32620-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/30/2023] [Indexed: 05/17/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a heterogeneous tumor that is highly aggressive and ranks fifth among the most common cancers worldwide. Although, the researches that attempted to construct a diagnostic model were deficient in HNSCC. Currently, the gold standard for diagnosing head and neck tumors is pathology, but this requires a traumatic biopsy. There is still a lack of a noninvasive test for such a high-incidence tumor. In order to screen genetic markers and construct diagnostic model, the methods of random forest (RF) and artificial neural network (ANN) were utilized. The data of HNSCC gene expression was accessed from Gene Expression Omnibus (GEO) database; we selected three datasets totally, and we combined 2 datasets (GSE6631 and GSE55547) for screening differentially expressed genes (DEGs) and chose another dataset (GSE13399) for validation. Firstly, the 6 DEGs (CRISP3, SPINK5, KRT4, MMP1, MAL, SPP1) were screened by RF. Subsequently, ANN was applied to calculate the weights of 6 genes. Besides, we created a diagnostic model and nominated it as neuralHNSCC, and the performance of neuralHNSCC by area under curve (AUC) was verified using another dataset. Our model achieved an AUC of 0.998 in the training cohort, and 0.734 in the validation cohort. Furthermore, we used the Cell-type Identification using Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm to investigate the difference in immune cell infiltration between HNSCC and normal tissues initially. The selected 6 DEGs and the constructed novel diagnostic model of HNSCC would make contributions to the diagnosis.
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Affiliation(s)
- Yao Luo
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Liu-Qing Zhou
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Fan Yang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jing-Cai Chen
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China
| | - Jian-Jun Chen
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
| | - Yan-Jun Wang
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430022, China.
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Liu J, Zhao J, Xu J, Sun Q, Qin X, Chen G, Gao T, Bai G, Guo Z. SPINK5 is a Prognostic Biomarker Associated With the Progression and Prognosis of Laryngeal Squamous Cell Carcinoma Identified by Weighted Gene Co-Expression Network Analysis. Evol Bioinform Online 2022; 18:11769343221077118. [PMID: 35140453 PMCID: PMC8819746 DOI: 10.1177/11769343221077118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 01/07/2022] [Indexed: 12/24/2022] Open
Abstract
Laryngeal squamous cell carcinoma (LSCC) is one of the most common types of head
and neck squamous cell carcinomas (HNSCC) and is the second most prevalent
malignancy occurring in the head and neck or respiratory tract, with a high
incidence and mortality rate. Survival is limited for patients with LSCC. To
identify more biomarkers associated with the prognosis of patients with LSCC,
using bioinformatics analysis, this study used The Cancer Genome Atlas (TCGA)
LSCC dataset and gene expression profiles of GSE59102 from the Gene Expression
Omnibus (GEO). Eighty-one differentially co-expressed genes were identified by
weighted gene co-expression network analysis (WGCNA). Next, 10 hub genes (PPL,
KRT78, CRNN, PTK7, SCEL, AGRN, SPINK5, AIF1L, EMP1, and PPP1R3C) were screened
from a protein-protein interaction (PPI) network. Based on survival analysis,
SPINK5 was significantly correlated with survival time in LSCC patients. After
verification in the TCGA and HPA databases, SPINK5 was selected as a prognostic
biomarker. Finally, the GSEA results showed that downregulation of SPINK5 gene
expression may promote tumorigenesis and the development of cancers by the
“BASAL CELL CARCINOMA” pathway, and it has been implicated in disrupting DNA
damage and repair pathways. Collectively, SPINK5 may serve as a potential
prognostic biomarker in LSCC.
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Affiliation(s)
- Jian Liu
- Department of Otolaryngology, Qingpu Branch of Zhongshan Hospital, Affiliated to Fudan University, Shanghai, P. R. China
| | - Jing Zhao
- Department of Otolaryngology, Qingpu Branch of Zhongshan Hospital, Affiliated to Fudan University, Shanghai, P. R. China
| | - Jiaran Xu
- Department of Ophthalmology, Qingpu Branch of Zhongshan Hospital, Affiliated to Fudan University, Shanghai, P. R. China
| | - Qing Sun
- Department of Otolaryngology, Qingpu Branch of Zhongshan Hospital, Affiliated to Fudan University, Shanghai, P. R. China
| | - Xuemei Qin
- Department of Otolaryngology, Qingpu Branch of Zhongshan Hospital, Affiliated to Fudan University, Shanghai, P. R. China
| | - Guohui Chen
- Department of Otolaryngology, Qingpu Branch of Zhongshan Hospital, Affiliated to Fudan University, Shanghai, P. R. China
| | - Tianle Gao
- Department of Otolaryngology, Qingpu Branch of Zhongshan Hospital, Affiliated to Fudan University, Shanghai, P. R. China
| | - Guangping Bai
- Department of Otolaryngology, Qingpu Branch of Zhongshan Hospital, Affiliated to Fudan University, Shanghai, P. R. China
| | - Zhiqiang Guo
- Department of Otolaryngology, Qingpu Branch of Zhongshan Hospital, Affiliated to Fudan University, Shanghai, P. R. China
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Walvekar VA, Ramesh K, Jobichen C, Kannan M, Sivaraman J, Kini RM, Mok YK. Crystal structure of Aedes aegypti trypsin inhibitor in complex with μ-plasmin reveals role for scaffold stability in Kazal-type serine protease inhibitor. Protein Sci 2022; 31:470-484. [PMID: 34800067 PMCID: PMC8820117 DOI: 10.1002/pro.4245] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 02/03/2023]
Abstract
Kazal-type protease inhibitor specificity is believed to be determined by sequence of the reactive-site loop that make most, if not all, contacts with the serine protease. Here, we determined the complex crystal structure of Aedes aegypti trypsin inhibitor (AaTI) with μ-plasmin, and compared its reactivities with other Kazal-type inhibitors, infestin-1 and infestin-4. We show that the shortened 99-loop of plasmin creates an S2 pocket, which is filled by phenylalanine at the P2 position of the reactive-site loop of infestin-4. In contrast, AaTI and infestin-1 retain a proline at P2, rendering the S2 pocket unfilled, which leads to lower plasmin inhibitions. Furthermore, the protein scaffold of AaTI is unstable, due to an elongated Cys-V to Cys-VI region leading to a less compact hydrophobic core. Chimeric study shows that the stability of the scaffold can be modified by swapping of this Cys-V to Cys-VI region between AaTI and infestin-4. The scaffold instability causes steric clashing of the bulky P2 residue, leading to significantly reduced inhibition of plasmin by AaTI or infestin-4 chimera. Our findings suggest that surface loops of protease and scaffold stability of Kazal-type inhibitor are both necessary for specific protease inhibition, in addition to reactive site loop sequence. PDB ID code: 7E50.
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Affiliation(s)
| | - Karthik Ramesh
- Department of Biological SciencesNational University of SingaporeSingapore,Present address:
Department of Biophysics and BiochemistryUT Southwestern Medical CentreDallasTXUSA
| | - Chacko Jobichen
- Department of Biological SciencesNational University of SingaporeSingapore
| | - Muthu Kannan
- Department of Biological SciencesNational University of SingaporeSingapore
| | - J. Sivaraman
- Department of Biological SciencesNational University of SingaporeSingapore
| | - R. Manjunatha Kini
- Department of Biological SciencesNational University of SingaporeSingapore,Department of PharmacologyYong Loo Lin School of Medicine, National University of SingaporeSingapore
| | - Yu Keung Mok
- Department of Biological SciencesNational University of SingaporeSingapore
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Ramesh K, Matta SA, Chew FT, Mok YK. Exonic mutations associated with atopic dermatitis disrupt lympho-epithelial Kazal-type related inhibitor action and enhance its degradation. Allergy 2020; 75:403-411. [PMID: 31407378 DOI: 10.1111/all.14018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/09/2019] [Accepted: 07/24/2019] [Indexed: 11/29/2022]
Abstract
BACKGROUND Skin desquamation is facilitated by serine proteases KLK5 and KLK7, which are tightly regulated by lympho-epithelial Kazal-type related inhibitor (LEKTI). LEKTI itself is controlled through degraded by mesotrypsin. Here, we sought to determine whether LEKTI exonic mutations associated with atopic dermatitis (AD) affect the protease inhibitory activity of LEKTI or its susceptibility to mesotrypsin degradation. METHODS The inhibitory activities of the LEKTI domain 4 (D4) and D6 WT and AD-associated mutants on the enzyme activities of KLK5 and KLK7 were compared using fluorogenic substrates. A keratinocyte cell culture system using HaCat cells was established to assess the role of D6 WT and D386N on triggering inflammation via the induction of thymic stromal lymphopoietin (TSLP). A degradation assay was used to assess the susceptibility of D4 and D6 mutants to mesotrypsin degradation. RESULTS Enzymatic assays revealed that the D6 D386N mutation affected the inhibitory activity of LEKTI on KLK5 but not KLK7. Other exonic mutations on D6 (N368S, V395M, and E420K) and D4 (R267Q) did not alter LEKTI inhibition. The D386N mutation disrupted the role of D6 in suppressing TSLP induction by KLK5 in HaCat cells. Although WT D4 is more susceptible to mesotrypsin degradation than WT D6, the D4 R267Q mutant was more resistant to mesotrypsin degradation, whereas the D6 E420K mutant showed enhanced mesotrypsin-mediated degradation. CONCLUSION Exonic mutations in D6, which previously have been associated with AD, may cause a disruption of inhibitory activity on KLK5 or enhance the degradation by mesotrypsin.
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Affiliation(s)
- Karthik Ramesh
- Department of Biological Sciences National University of Singapore Singapore City Singapore
| | - Sri Anusha Matta
- Department of Biological Sciences National University of Singapore Singapore City Singapore
| | - Fook Tim Chew
- Department of Biological Sciences National University of Singapore Singapore City Singapore
| | - Yu Keung Mok
- Department of Biological Sciences National University of Singapore Singapore City Singapore
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