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Liu H, Dang R, Zhang W, Hong J, Li X. SNARE proteins: Core engines of membrane fusion in cancer. Biochim Biophys Acta Rev Cancer 2024:189148. [PMID: 38960006 DOI: 10.1016/j.bbcan.2024.189148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 06/23/2024] [Accepted: 06/27/2024] [Indexed: 07/05/2024]
Abstract
Vesicles are loaded with a variety of cargoes, including membrane proteins, secreted proteins, signaling molecules, and various enzymes, etc. Not surprisingly, vesicle transport is essential for proper cellular life activities including growth, division, movement and cellular communication. Soluble N-ethylmaleimide-sensitive factor attachment protein receptors (SNAREs) mediate membrane fusion of vesicles with their target compartments that is fundamental for cargo delivery. Recent studies have shown that multiple SNARE family members are aberrantly expressed in human cancers and actively contribute to malignant proliferation, invasion, metastasis, immune evasion and treatment resistance. Here, the localization and function of SNARE proteins in eukaryotic cells are firstly mapped. Then we summarize the expression and regulation of SNAREs in cancer, and describe their contribution to cancer progression and mechanisms, and finally we propose engineering botulinum toxin as a strategy to target SNAREs for cancer treatment.
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Affiliation(s)
- Hongyi Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China; Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Ruiyue Dang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China; Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Jidong Hong
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China.
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China; Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China.
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Zhang R, Zhao W, Zhu X, Liu Y, Ding Q, Yang C, Zou H. Identification of hub genes distinguishing subtypes in endometrial stromal sarcoma through comprehensive bioinformatics analysis. Sci Rep 2024; 14:37. [PMID: 38167455 PMCID: PMC10761685 DOI: 10.1038/s41598-023-47668-7] [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: 05/21/2023] [Accepted: 11/16/2023] [Indexed: 01/05/2024] Open
Abstract
Diagnosing low-grade and high-grade endometrial stromal sarcoma (LG-ESS and HG-ESS) is a challenge. This study aimed to identify biomarkers. 22 ESS cases were analyzed using Illumina microarrays. Differentially expressed genes (DEGs) were identified via Limma. DEGs were analyzed with String and Cytoscape. Core genes were enriched with GO and KEGG, their pan-cancer implications and immune aspects were studied. 413 DEGs were found by exome sequencing, 2174 by GSE85383 microarray. 36 common genes were identified by Venn analysis, and 10 core genes including RBFOX1, PCDH7, FAT1 were selected. Core gene GO enrichment included cell adhesion, T cell proliferation, and KEGG focused on related pathways. Expression was evaluated across 34 cancers, identifying immune DEGs IGF1 and AVPR1A. Identifying the DEGs not only helps improve our understanding of LG-ESS, HG-ESS but also promises to be potential biomarkers for differential diagnosis between LG-ESS and HG-ESS and new therapeutic targets.
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Affiliation(s)
- Ruiqi Zhang
- Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Weilin Zhao
- Department of Pathology, Taihe Hospital, Hubei University of Medicine, Hubei, 442000, China
| | - Xingyao Zhu
- Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang, 310009, China
| | - Yuhua Liu
- Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Qi Ding
- Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Caiyun Yang
- Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Xinjiang, 832002, China
| | - Hong Zou
- Department of Pathology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang, 310009, China.
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Yin L, Xu Y, Yin J, Cheng H, Xiao W, Wu Y, Ji D, Gao S. Construction and validation of a risk model based on the key SNARE proteins to predict the prognosis and immune microenvironment of gliomas. Front Mol Neurosci 2023; 16:1304224. [PMID: 38115820 PMCID: PMC10728289 DOI: 10.3389/fnmol.2023.1304224] [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: 09/29/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
Background Synaptic transmission between neurons and glioma cells can promote glioma progression. The soluble N-ethylmaleimide-sensitive fusion factor attachment protein receptors (SNARE) play a key role in synaptic functions. We aimed to construct and validate a novel model based on the SNARE proteins to predict the prognosis and immune microenvironment of glioma. Methods Differential expression analysis and COX regression analysis were used to identify key SRGs in glioma datasets, and we constructed a prognostic risk model based on the key SRGs. The prognostic value and predictive performance of the model were assessed in The Cancer Genome Atlas (TCGA) and Chinese glioma Genome Atlas (CGGA) datasets. Functional enrichment analysis and immune-related evaluation were employed to reveal the association of risk scores with tumor progression and microenvironment. A prognostic nomogram containing the risk score was established and assessed by calibration curves and time-dependent receiver operating characteristic curves. We verified the changes of the key SRGs in glioma specimens and cells by real-time quantitative PCR and Western blot analyses. Results Vesicle-associated membrane protein 2 (VAMP2) and vesicle-associated membrane protein 5 (VAMP5) were identified as two SRGs affecting the prognoses of glioma patients. High-risk patients characterized by higher VAMP5 and lower VAMP2 expression had a worse prognosis. Higher risk scores were associated with older age, higher tumor grades, IDH wild-type, and 1p19q non-codeletion. The SRGs risk model showed an excellent predictive performance in predicting the prognosis in TCGA and CGGA datasets. Differentially expressed genes between low- and high-risk groups were mainly enriched in the pathways related to immune infiltration, tumor metastasis, and neuronal activity. Immune score, stromal score, estimate score, tumor mutational burden, and expression of checkpoint genes were positively correlated with risk scores. The nomogram containing the risk score showed good performance in predicting the prognosis of glioma. Low VAMP2 and high VAMP5 were found in different grades of glioma specimens and cell lines. Conclusion We constructed and validated a novel risk model based on the expression of VAMP2 and VAMP5 by bioinformatics analysis and experimental confirmation. This model might be helpful for clinically predicting the prognosis and response to immunotherapy of glioma patients.
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Affiliation(s)
- Luxin Yin
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Yiqiang Xu
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Jiale Yin
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Hai Cheng
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Weihan Xiao
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Yue Wu
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
- Department of Neurosurgery, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Daofei Ji
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
- Department of Neurosurgery, The Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Shangfeng Gao
- Department of Neurosurgery, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
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Shinozuka T, Kanda M, Sato Y, Shimizu D, Tanaka C, Umeda S, Inokawa Y, Hattori N, Hayashi M, Nakayama G, Kodera Y. Increased STX3 transcript and protein levels were associated with poor prognosis in two independent cohorts of esophageal squamous cell carcinoma patients. Cancer Med 2023; 12:22185-22195. [PMID: 38014487 PMCID: PMC10757105 DOI: 10.1002/cam4.6770] [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: 05/31/2023] [Revised: 11/07/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Some conventional prognostic biomarkers for esophageal squamous cell carcinoma (ESCC) have the disadvantage that they have only been investigated at the level of either mRNA or protein levels or only in individual cohorts. Associations between Syntaxin 3 (STX3) expression and malignancy have been reported in several tumor types but not in ESCC. Here, we investigated the levels of both STX3 mRNA and protein, and its prognostic potential in two independent cohorts of patients with ESCC. METHODS STX3 mRNA levels were examined in surgical specimens by quantitative PCR in a cohort that included 176 ESCC patients. STX3 protein levels were investigated in surgically resected ESCC tissues by immunohistochemistry using tissue microarrays in a different cohort of 177 ESCC patients. Correlations were analyzed between the expression of STX3 mRNA and protein with clinicopathological factors and long-term prognosis. RESULTS Quantitative PCR indicated a significant association between high level of STX3 mRNA expression and lymph node involvement, pathological stage, and poor overall survival. The multivariate analysis demonstrated that high STX3 mRNA expression was independently associated with poor overall survival outcomes. Immunohistochemistry revealed that STX3 protein expression in ESCC tissues and high STX3 protein expression were also significantly correlated with unfavorable overall survival. CONCLUSIONS Overexpression of STX3 mRNA and protein may serve as potential prognostic biomarkers for ESCC patients.
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Affiliation(s)
- Takahiro Shinozuka
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Mitsuro Kanda
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Yusuke Sato
- Department of Thoracic SurgeryAkita University Graduate School of MedicineAkitaJapan
| | - Dai Shimizu
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Chie Tanaka
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Shinichi Umeda
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Yoshikuni Inokawa
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Norifumi Hattori
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Masamichi Hayashi
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Goro Nakayama
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
| | - Yasuhiro Kodera
- Department of Gastroenterological SurgeryNagoya University Graduate School of MedicineNagoyaJapan
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Zhang Y, Lyu Y, Chen L, Cao K, Chen J, He C, Lyu X, Jiang Y, Xiang J, Liu B, Wu C. Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS. Int J Mol Sci 2023; 24:15259. [PMID: 37894938 PMCID: PMC10607287 DOI: 10.3390/ijms242015259] [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: 08/08/2023] [Revised: 09/30/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
The use of metabolome genome-wide association studies (mGWAS) has been shown to be effective in identifying functional genes in complex diseases. While mGWAS has been applied to biomedical and pharmaceutical studies, its potential in predicting gastric cancer prognosis has yet to be explored. This study aims to address this gap and provide insights into the genetic basis of GC survival, as well as identify vital regulatory pathways in GC cell progression. Genome-wide association analysis of plasma metabolites related to gastric cancer prognosis was performed based on the Generalized Linear Model (GLM). We used a log-rank test, LASSO regression, multivariate Cox regression, GO enrichment analysis, and the Cytoscape software to visualize the complex regulatory network of genes and metabolites and explored in-depth genetic variation in gastric cancer prognosis based on mGWAS. We found 32 genetic variation loci significantly associated with GC survival-related metabolites, corresponding to seven genes, VENTX, PCDH 7, JAKMIP1, MIR202HG, MIR378D1, LINC02472, and LINC02310. Furthermore, this study identified 722 Single nucleotide polymorphism (SNP) sites, suggesting an association with GC prognosis-related metabolites, corresponding to 206 genes. These 206 possible functional genes for gastric cancer prognosis were mainly involved in cellular signaling molecules related to cellular components, which are mainly involved in the growth and development of the body and neurological regulatory functions related to the body. The expression of 23 of these genes was shown to be associated with survival outcome in gastric cancer patients in The Cancer Genome Atlas (TCGA) database. Based on the genome-wide association analysis of prognosis-related metabolites in gastric cancer, we suggest that gastric cancer survival-related genes may influence the proliferation and infiltration of gastric cancer cells, which provides a new idea to resolve the complex regulatory network of gastric cancer prognosis.
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Affiliation(s)
- Yuling Zhang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Yanping Lyu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Liangping Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Kang Cao
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Jingwen Chen
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Chenzhou He
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Xuejie Lyu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Yu Jiang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Jianjun Xiang
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Baoying Liu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
| | - Chuancheng Wu
- Department of Preventive Medicine, School of Public Health, Fujian Medical University, Fuzhou 350108, China; (Y.Z.); (Y.L.); (L.C.); (K.C.); (J.C.); (C.H.); (X.L.); (Y.J.); (J.X.); (B.L.)
- The Key Laboratory of Environment and Health, School of Public Health, Fujian Medical University, Fuzhou 350108, China
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Amgalan B, Day CP, Przytycka TM. Exploring tumor-normal cross-talk with TranNet: Role of the environment in tumor progression. PLoS Comput Biol 2023; 19:e1011472. [PMID: 37721939 PMCID: PMC10538798 DOI: 10.1371/journal.pcbi.1011472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/28/2023] [Accepted: 08/23/2023] [Indexed: 09/20/2023] Open
Abstract
There is a growing awareness that tumor-adjacent normal tissues used as control samples in cancer studies do not represent fully healthy tissues. Instead, they are intermediates between healthy tissues and tumors. The factors that contribute to the deviation of such control samples from healthy state include exposure to the tumor-promoting factors, tumor-related immune response, and other aspects of tumor microenvironment. Characterizing the relation between gene expression of tumor-adjacent control samples and tumors is fundamental for understanding roles of microenvironment in tumor initiation and progression, as well as for identification of diagnostic and prognostic biomarkers for cancers. To address the demand, we developed and validated TranNet, a computational approach that utilizes gene expression in matched control and tumor samples to study the relation between their gene expression profiles. TranNet infers a sparse weighted bipartite graph from gene expression profiles of matched control samples to tumors. The results allow us to identify predictors (potential regulators) of this transition. To our knowledge, TranNet is the first computational method to infer such dependencies. We applied TranNet to the data of several cancer types and their matched control samples from The Cancer Genome Atlas (TCGA). Many predictors identified by TranNet are genes associated with regulation by the tumor microenvironment as they are enriched in G-protein coupled receptor signaling, cell-to-cell communication, immune processes, and cell adhesion. Correspondingly, targets of inferred predictors are enriched in pathways related to tissue remodelling (including the epithelial-mesenchymal Transition (EMT)), immune response, and cell proliferation. This implies that the predictors are markers and potential stromal facilitators of tumor progression. Our results provide new insights into the relationships between tumor adjacent control sample, tumor and the tumor environment. Moreover, the set of predictors identified by TranNet will provide a valuable resource for future investigations.
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Affiliation(s)
- Bayarbaatar Amgalan
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chi-Ping Day
- Laboratory of Cancer Biology and Genetics/Center for Cancer Research/National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Teresa M. Przytycka
- National Center for Biotechnology Information/National Library of Medicine, National Institutes of Health, Bethesda, Maryland, United States of America
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Wang X, Luo X, Wang Z, Wang Y, Zhao J, Bian L. Identification of cancer stemness and M2 macrophage-associated biomarkers in lung adenocarcinoma. Heliyon 2023; 9:e19114. [PMID: 37662825 PMCID: PMC10472008 DOI: 10.1016/j.heliyon.2023.e19114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 08/06/2023] [Accepted: 08/10/2023] [Indexed: 09/05/2023] Open
Abstract
Objective Cancer stemness and M2 macrophages are intimately linked to the prognosis of lung adenocarcinoma (LUAD). For this reason, this investigation sought to identify the key genes relevant to cancer stemness and M2 macrophages, explore the relationship between these genes and clinical characteristics, and determine the potential mechanism. Methods LUAD transcriptomic data was analyzed from The Cancer Genome Atlas (TCGA) as well as the Gene Expression Omnibus databases. Differential expression analysis was performed to discern abnormally expressed genes between LUAD and control samples in TCGA cohort. The Cell type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was applied to determine varyingly infiltrated immune cells in LUAD compared with the control samples in TCGA cohort. Weighted correlation network analysis (WGCNA) was performed to identify genes associated with mRNA expression-based stemness index (mRNAsi) and M2 macrophages. Least absolute shrinkage and selection operator (LASSO), RandomForest (RF) and support vector machine-recursive feature elimination (SVM-RFE) machine learning methods were conducted to detect gene signatures. Global survival evaluation (Kaplan-Meier curve) was applied to investigate the relationship between gene signatures and the survival time of LUAD patients. Receiver operating characteristic (ROC) curves were produced to define biomarkers relevant to diagnosis. Gene Set Enrichment Analysis (GSEA) was performed to probe the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to diagnostic biomarkers. The public single-cell dataset of LUAD (GSE123902) was used to investigate the expression differences of diagnostic biomarkers in various cell types in LUAD. Real-time quantitative PCR (qRT-PCR) was performed to confirm key genes in lung adenocarcinoma cells. Results A total of 5,410 differentialy expressed genes (DEGs) as well as 15 differentially infiltrated immune cells were identified between LUAD and control sepcimens in TCGA cohort. Thirty-seven DEGs were associated with both M2 macrophages and mRNAsi according to the WGCNA analysis. Sixteen common gene signatures were obtained using three diverse algorithms. CBFA2T3, DENND3 and FCAMR were correlated to overall and disease-free survival of LUAD patients. ROC curves revealed that CBFA2T3 and DENND3 expression accurately classified LUAD and control samples. The results of single cell related analysis showed that two diagnostic biomarkers expressions were differed between the different tissue sources in M2-like macrophages. QRT-PCR demonstrated the mRNA expressions of CBFA2T3 and DENND3 were upregulated in lung adenocarcinoma cells A549 and H2122. Conclusion Our study identified CBFA2T3 and DENND3 as key genes associated with mRNAsi and M2 macrophages in LUAD and investigated the potential molecular mechanisms underlying this relationship.
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Affiliation(s)
| | | | - ZhiYuan Wang
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - YangHao Wang
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Juan Zhao
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Bian
- The First Affiliated Hospital of Kunming Medical University, Kunming, China
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Xie X, Kong S, Cao W. Targeting protein glycosylation to regulate inflammation in the respiratory tract: novel diagnostic and therapeutic candidates for chronic respiratory diseases. Front Immunol 2023; 14:1168023. [PMID: 37256139 PMCID: PMC10225578 DOI: 10.3389/fimmu.2023.1168023] [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: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/01/2023] Open
Abstract
Protein glycosylation is a widespread posttranslational modification that can impact the function of proteins. Dysregulated protein glycosylation has been linked to several diseases, including chronic respiratory diseases (CRDs). CRDs pose a significant public health threat globally, affecting the airways and other lung structures. Emerging researches suggest that glycosylation plays a significant role in regulating inflammation associated with CRDs. This review offers an overview of the abnormal glycoenzyme activity and corresponding glycosylation changes involved in various CRDs, including chronic obstructive pulmonary disease, asthma, cystic fibrosis, idiopathic pulmonary fibrosis, pulmonary arterial hypertension, non-cystic fibrosis bronchiectasis, and lung cancer. Additionally, this review summarizes recent advances in glycomics and glycoproteomics-based protein glycosylation analysis of CRDs. The potential of glycoenzymes and glycoproteins for clinical use in the diagnosis and treatment of CRDs is also discussed.
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Affiliation(s)
- Xiaofeng Xie
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Siyuan Kong
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Weiqian Cao
- Shanghai Fifth People’s Hospital and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- NHC Key Laboratory of Glycoconjugates Research, Fudan University, Shanghai, China
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Zheng Z, Luan N, Tu K, Liu F, Wang J, Sun J. The roles of protocadherin-7 in colorectal cancer cells on cell proliferation and its chemoresistance. Front Pharmacol 2023; 14:1072033. [PMID: 37063257 PMCID: PMC10098175 DOI: 10.3389/fphar.2023.1072033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/09/2023] [Indexed: 04/18/2023] Open
Abstract
Despite the high mutation frequencies of KRAS, NRAS, and BRAF in colorectal cancer (CRC), there are no effective and reliable inhibitors for these biomarkers. Protocadherin-7 (PCDH7) is regarded as a potentially targetable surface molecule in cancer cells and plays an important role in their proliferation, metastasis, and drug resistance. However, the roles and underlying mechanisms of PCDH7 in CRC remain unclear. In the current study, we found that different colorectal cancer cells expressed PCDH7 over a wide range. The levels of PCDH7 expression were positively associated with cell proliferation and drug resistance in CRC cells but negatively correlated with the potential for cell migration and invasion. Our data indicated that PCDH7 mediated the resistance of CRC cells to ABT-263 (a small-molecule Bcl-2 inhibitor that induces apoptosis) by inhibiting cell apoptosis, which was supported by the downregulation of caspase-3, caspase-9, and PARP cleavage. We found that PCDH7 effectively promoted Mcl-1 expression at both mRNA and protein levels. Furthermore, PCDH7 activated the Wnt signaling pathway, which was confirmed by the increase in β-catenin and c-Myc expression. Finally, and notably, S63845, a novel Mcl-1 inhibitor, not only effectively attenuated the inhibitory effect of PCDH7 on cell apoptosis induced by ABT-263 in vitro but also sensitized PCDH7-overexpressed CRC cell-derived xenografts to ABT-263 in vivo. Taken together, although PCDH7 inhibited the migration and invasion of CRC cells, it could facilitate the development of drug resistance in colorectal cancer cells by positively modulating Mcl-1 expression. The application of the Mcl-1 inhibitor S63845 could be a potential strategy for CRC chemotherapy, especially in CRC with high levels of PCDH7.
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Affiliation(s)
- Zhibao Zheng
- Department of Surgical Oncology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
| | - Na Luan
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kai Tu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Feiyan Liu
- College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jianwei Wang
- Department of Colorectal Surgery and Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- *Correspondence: Jianguo Sun, ; Jianwei Wang,
| | - Jianguo Sun
- Department of Surgical Oncology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, Zhejiang, China
- *Correspondence: Jianguo Sun, ; Jianwei Wang,
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Guan Q, Zhao P, Tian Y, Yang L, Zhang Z, Li J. Identification of cancer risk assessment signature in patients with chronic obstructive pulmonary disease and exploration of the potential key genes. Ann Med 2022; 54:2309-2320. [PMID: 35993327 PMCID: PMC9415445 DOI: 10.1080/07853890.2022.2112070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
It is essential to assess the cancer risk for patients with chronic obstructive pulmonary disease (COPD). Comparing gene expression data from patients with lung cancer (a total of 506 samples) and those with cancer-adjacent normal lung tissues (a total of 370 samples), we generated a qualitative transcriptional signature consisting of 2046 gene pairs. The signature was verified in an evaluation dataset comprising 18 subjects with severe disease and 52 subjects with moderate disease (Wilcoxon rank-sum test; p = 7.33 × 10-5). Similar results were obtained in other independent datasets. Among the gene pairs in the signature, 326 COPD stage-related gene pairs were identified based on Spearman's rank correlation tests and those gene pairs comprised 368 unique genes. Of these 368 genes, 16 genes were significantly dysregulated in COPD rat model data compared with control data. Some of these genes (Dhx16, Upf2, Notch3, Sec61a1, Dyrk2, and Hmmr) were altered when the COPD rat model was treated with traditional Chinese medicines (TCM), including Bufei Yishen formula, Bufei Jianpi formula, and Yiqi Zishen formula. Overall, the signature could predict the cancer incidence-risk of COPD and the identified key genes might provide guidance regarding both the treatment of COPD using TCM and the prevention of cancer in patients with COPD. KEY MESSAGESA cancer risk assessment signature was identified in patients with COPD.The signature is insensitive to batch effects and is well verified.COPD key genes identified in this study might play a crucial role in TCM treatment and cancer prevention.
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Affiliation(s)
- Qingzhou Guan
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China.,Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou, China
| | - Peng Zhao
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China.,Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou, China
| | - Yange Tian
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China.,Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou, China
| | - Liping Yang
- School of Basic Medicine, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zhenzhen Zhang
- Academy of Chinese Medical Sciences, Henan University of Chinese Medicine, Zhengzhou, China.,Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jiansheng Li
- Henan Key Laboratory of Chinese Medicine for Respiratory Disease, Co-Construction Collaborative Innovation Center for Chinese Medicine and Respiratory Diseases by Henan & Education Ministry of P.R. China, Henan University of Chinese Medicine, Zhengzhou, China.,The First Affiliated Hospital, Henan University of Chinese Medicine, Zhengzhou, China
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11
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Nai A, Ma F, He Z, Zeng S, Bashir S, Song J, Xu M. Development and Validation of a 7-Gene Inflammatory Signature Forecasts Prognosis and Diverse Immune Landscape in Lung Adenocarcinoma. Front Mol Biosci 2022; 9:822739. [PMID: 35372503 PMCID: PMC8964604 DOI: 10.3389/fmolb.2022.822739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/15/2022] [Indexed: 11/20/2022] Open
Abstract
Background: Inflammatory responses are strongly linked with tumorigenesis and cancer development. This research aimed to construct and validate a novel inflammation response–related risk predictive signature for forecasting the prognosis of patients with LUAD. Methods: Differential expression analysis, univariate Cox, LASSO, and multivariate Cox regression analyses of 200 inflammatory response–related genes (IRRG) were performed to establish a risk predictive model in the TCGA training cohort. The performance of the IRRG model was verified in eight GEO datasets. GSEA analysis, ESTIMATE algorithms, and ssGSEA analysis were applied to elucidate the possible mechanisms. Furthermore, the relationship analysis between risk score, model genes, and chemosensitivity was performed. Last, we verified the protein expression of seven model genes by immunohistochemical staining or Western blotting. Results: We constructed a novel inflammatory response–related 7-gene signature (MMP14, BTG2, LAMP3, CCL20, TLR2, IL7R, and PCDH7). Patients in the high-risk group presented markedly decreased survival time in the TCGA cohort and eight GEO cohorts than the low-risk group. Interestingly, multiple pathways related to immune response were suppressed in high-risk groups. The low infiltration levels of B cell, dendritic cell, natural killer cell, and eosinophil can significantly affect the unsatisfactory prognosis of the high-risk group in LUAD. Moreover, the tumor cells’ sensitivity to anticancer drugs was markedly related to risk scores and model genes. The protein expression of seven model genes was consistent with the mRNA expression. Conclusion: Our IRRG prognostic model can effectively forecast LUAD prognosis and is tightly related to immune infiltration.
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Affiliation(s)
- Aitao Nai
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Feng Ma
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Zirui He
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Shuwen Zeng
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Shoaib Bashir
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Jian Song
- Department of Oncology, ZhongShan Torch Development Zone Hospital, Zhongshan, China
- *Correspondence: Meng Xu, ; Jian Song,
| | - Meng Xu
- Department of Oncology, The First Affiliated Hospital of Jinan University, Guangzhou, China
- *Correspondence: Meng Xu, ; Jian Song,
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12
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Xu R, Lu T, Zhao J, Wang J, Peng B, Zhang L. Identification of Tumor Antigens and Immune Subtypes in Lung Adenocarcinoma for mRNA Vaccine Development. Front Cell Dev Biol 2022; 10:815596. [PMID: 35265614 PMCID: PMC8899518 DOI: 10.3389/fcell.2022.815596] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 01/31/2022] [Indexed: 12/18/2022] Open
Abstract
Cancer vaccines are emerging as a viable strategy for cancer treatment. In the current study, we screened for genes associated with the prognosis of patients with lung adenocarcinoma and positively correlated with antigen-presenting cell infiltration and identified KLRG1 and CBFA2T3 as potential tumor antigens for mRNA vaccines in lung adenocarcinoma (LUAD). Further analyses of immune subtypes revealed that patients with early-stage LUAD, high immune cell infiltration, high immune checkpoint expression, and low tumor mutation burden might benefit from mRNA vaccination. Moreover, we identified four biomarkers that can be used to assess mRNA vaccination suitability. We also identified potentially sensitive anti-cancer drugs for populations not suitable for vaccination by means of anti-cancer drug susceptibility prediction. Overall, we provided a new perspective for mRNA vaccine treatment strategies for LUAD and emphasized the importance of precise and personalized treatments.
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Affiliation(s)
- Ran Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Harbin Medical University, Harbin, China
| | - Tong Lu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Harbin Medical University, Harbin, China
| | - JiaYing Zhao
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Harbin Medical University, Harbin, China
| | - Jun Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Harbin Medical University, Harbin, China
| | - Bo Peng
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China.,Harbin Medical University, Harbin, China
| | - LinYou Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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13
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Elling CL, Scholes MA, Streubel SO, Larson ED, Wine TM, Bootpetch TC, Yoon PJ, Kofonow JM, Gubbels SP, Cass SP, Robertson CE, Jenkins HA, Prager JD, Frank DN, Chan KH, Friedman NR, Ryan AF, Santos-Cortez RLP. The FUT2 Variant c.461G>A (p.Trp154*) Is Associated With Differentially Expressed Genes and Nasopharyngeal Microbiota Shifts in Patients With Otitis Media. Front Cell Infect Microbiol 2022; 11:798246. [PMID: 35096646 PMCID: PMC8798324 DOI: 10.3389/fcimb.2021.798246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/20/2021] [Indexed: 12/30/2022] Open
Abstract
Otitis media (OM) is a leading cause of childhood hearing loss. Variants in FUT2, which encodes alpha-(1,2)-fucosyltransferase, were identified to increase susceptibility to OM, potentially through shifts in the middle ear (ME) or nasopharyngeal (NP) microbiotas as mediated by transcriptional changes. Greater knowledge of differences in relative abundance of otopathogens in carriers of pathogenic variants can help determine risk for OM in patients. In order to determine the downstream effects of FUT2 variation, we examined gene expression in relation to carriage of a common pathogenic FUT2 c.461G>A (p.Trp154*) variant using RNA-sequence data from saliva samples from 28 patients with OM. Differential gene expression was also examined in bulk mRNA and single-cell RNA-sequence data from wildtype mouse ME mucosa after inoculation with non-typeable Haemophilus influenzae (NTHi). In addition, microbiotas were profiled from ME and NP samples of 65 OM patients using 16S rRNA gene sequencing. In human carriers of the FUT2 variant, FN1, KMT2D, MUC16 and NBPF20 were downregulated while MTAP was upregulated. Post-infectious expression in the mouse ME recapitulated these transcriptional differences, with the exception of Fn1 upregulation after NTHi-inoculation. In the NP, Candidate Division TM7 was associated with wildtype genotype (FDR-adj-p=0.009). Overall, the FUT2 c.461G>A variant was associated with transcriptional changes in processes related to response to infection and with increased load of potential otopathogens in the ME and decreased commensals in the NP. These findings provide increased understanding of how FUT2 variants influence gene transcription and the mucosal microbiota, and thus contribute to the pathology of OM.
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Affiliation(s)
- Christina L. Elling
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Melissa A. Scholes
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Sven-Olrik Streubel
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Eric D. Larson
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Todd M. Wine
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Tori C. Bootpetch
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Patricia J. Yoon
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Jennifer M. Kofonow
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Samuel P. Gubbels
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Stephen P. Cass
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Charles E. Robertson
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Herman A. Jenkins
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Jeremy D. Prager
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Daniel N. Frank
- Division of Infectious Diseases, Department of Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
| | - Kenny H. Chan
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Norman R. Friedman
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Department of Pediatric Otolaryngology, Children’s Hospital Colorado, Aurora, CO, United States
| | - Allen F. Ryan
- Division of Otolaryngology, Department of Surgery, San Diego School of Medicine and Veterans Affairs Medical Center, University of California, La Jolla, CA, United States
| | - Regie Lyn P. Santos-Cortez
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Human Medical Genetics and Genomics Program, University of Colorado Anschutz Medical Campus, Aurora, CO, United States
- Center for Children’s Surgery, Children’s Hospital Colorado, Aurora, CO, United States
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