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Chen Q, Zhao H, Hu J. A robust six-gene prognostic signature based on two prognostic subtypes constructed by chromatin regulators is correlated with immunological features and therapeutic response in lung adenocarcinoma. Aging (Albany NY) 2023; 15:12330-12368. [PMID: 37938151 PMCID: PMC10683604 DOI: 10.18632/aging.205183] [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: 02/20/2023] [Accepted: 10/02/2023] [Indexed: 11/09/2023]
Abstract
Accumulating evidence has demonstrated that chromatin regulators (CRs) regulate immune cell infiltration and are correlated with prognoses of patients in some cancers. However, the immunological and prognostic roles of CRs in lung adenocarcinoma (LUAD) are still unclear. Here, we systematically revealed the correlations of CRs with immunological features and the survival in LUAD patients based on a cohort of gene expression datasets from the public TCGA and GEO databases and real RNA-seq data by an integrative analysis using a comprehensive bioinformatics method. Totals of 160 differentially expressed CRs (DECRs) were identified between LUAD and normal lung tissues, and two molecular prognostic subtypes (MPSs) were constructed and evaluated based on 27 prognostic DECRs using five independent datasets (p =0.016, <0.0001, =0.008, =0.00038 and =0.00055, respectively). Six differentially expressed genes (DEGs) (CENPK, ANGPTL4, CCL20, CPS1, GJB3, TPSB2) between two MPSs had the most important prognostic feature and a six-gene prognostic model was established. LUAD patients in the low-risk subgroup showed a higher overall survival (OS) rate than those in the high-risk subgroup in nine independent datasets (p <0.0001, =0.021, =0.016, =0.0099, <0.0001, =0.0045, <0.0001, =0.0038 and =0.00013, respectively). Six-gene prognostic signature had the highest concordance index of 0.673 compared with 19 reported prognostic signatures. The risk score was significantly correlated with immunological features and activities of oncogenic signaling pathways. LUAD patients in the low-risk subgroup benefited more from immunotherapy and were less sensitive to conventional chemotherapy agents. This study provides novel insights into the prognostic and immunological roles of CRs in LUAD.
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Affiliation(s)
- Qiang Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Hongbo Zhao
- Department of Laboratory Animal Science, Kunming Medical University, Kunming, China
| | - Jing Hu
- Department of Medical Oncology, First People’s Hospital of Yunnan Province, Kunming, China
- Department of Medical Oncology, Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
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Feng F, Zhong YX, Huang JH, Lin FX, Zhao PP, Mai Y, Wei W, Zhu HC, Xu ZP. Identifying stage-associated hub genes in bladder cancer via weighted gene co-expression network and robust rank aggregation analyses. Medicine (Baltimore) 2022; 101:e32318. [PMID: 36595851 PMCID: PMC9794320 DOI: 10.1097/md.0000000000032318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Bladder cancer (BC) is among the most frequent cancers globally. Although substantial efforts have been put to understand its pathogenesis, its underlying molecular mechanisms have not been fully elucidated. METHODS The robust rank aggregation approach was adopted to integrate 4 eligible bladder urothelial carcinoma microarray datasets from the Gene Expression Omnibus. Differentially expressed gene sets were identified between tumor samples and equivalent healthy samples. We constructed gene co-expression networks using weighted gene co-expression network to explore the alleged relationship between BC clinical characteristics and gene sets, as well as to identify hub genes. We also incorporated the weighted gene co-expression network and robust rank aggregation to screen differentially expressed genes. RESULTS CDH11, COL6A3, EDNRA, and SERPINF1 were selected from the key module and validated. Based on the results, significant downregulation of the hub genes occurred during the early stages of BC. Moreover, receiver operating characteristics curves and Kaplan-Meier plots showed that the genes exhibited favorable diagnostic and prognostic value for BC. Based on gene set enrichment analysis for single hub gene, all the genes were closely linked to BC cell proliferation. CONCLUSIONS These results offer unique insight into the pathogenesis of BC and recognize CDH11, COL6A3, EDNRA, and SERPINF1 as potential biomarkers with diagnostic and prognostic roles in BC.
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Affiliation(s)
- Fu Feng
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Yu-Xiang Zhong
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Jian-Hua Huang
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Fu-Xiang Lin
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Peng-Peng Zhao
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Yuan Mai
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Wei Wei
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Hua-Cai Zhu
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
| | - Zhan-Ping Xu
- Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, Foshan, China
- * Correspondence: Zhan-Ping Xu, Department of Urinary Surgery, Foshan Hospital of Traditional Chinese Medicine, 6 Qinren Road, Foshan 528099, China (e-mail: )
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Jung M, Lee C, Han D, Kim K, Yang S, Nikas IP, Moon KC, Kim H, Song MJ, Kim B, Lee H, Ryu HS. Proteomic-Based Machine Learning Analysis Reveals PYGB as a Novel Immunohistochemical Biomarker to Distinguish Inverted Urothelial Papilloma From Low-Grade Papillary Urothelial Carcinoma With Inverted Growth. Front Oncol 2022; 12:841398. [PMID: 35402263 PMCID: PMC8987228 DOI: 10.3389/fonc.2022.841398] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundThe molecular biology of inverted urothelial papilloma (IUP) as a precursor disease of urothelial carcinoma is poorly understood. Furthermore, the overlapping histology between IUP and papillary urothelial carcinoma (PUC) with inverted growth is a diagnostic pitfall leading to frequent misdiagnoses.MethodsTo identify the oncologic significance of IUP and discover a novel biomarker for its diagnosis, we employed mass spectrometry-based proteomic analysis of IUP, PUC, and normal urothelium (NU). Machine learning analysis shortlisted candidate proteins, while subsequent immunohistochemical validation was performed in an independent sample cohort.ResultsFrom the overall proteomic landscape, we found divergent ‘NU-like’ (low-risk) and ‘PUC-like’ (high-risk) signatures in IUP. The latter were characterized by altered metabolism, biosynthesis, and cell–cell interaction functions, indicating oncologic significance. Further machine learning-based analysis revealed SERPINH1, PKP2, and PYGB as potential diagnostic biomarkers discriminating IUP from PUC. The immunohistochemical validation confirmed PYGB as a specific biomarker to distinguish between IUP and PUC with inverted growth.ConclusionIn conclusion, we suggest PYGB as a promising immunohistochemical marker for IUP diagnosis in routine practice.
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Affiliation(s)
- Minsun Jung
- Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea
- Department of Pathology, Severance Hospital, Yonsei University College of Medicine, Seoul, South Korea
| | - Cheol Lee
- Department of Pathology, Seoul National University Hospital, Seoul, South Korea
| | - Dohyun Han
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, South Korea
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Kwangsoo Kim
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, South Korea
| | - Sunah Yang
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul, South Korea
| | - Ilias P. Nikas
- School of Medicine, European University Cyprus, Nicosia, Cyprus
| | - Kyung Chul Moon
- Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea
- Department of Pathology, Seoul National University Hospital, Seoul, South Korea
- Kidney Research Institute, Medical Research Center, Seoul National University College of Medicine, Seoul, South Korea
| | - Hyeyoon Kim
- Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Min Ji Song
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
| | - Bohyun Kim
- Department of Pathology, Konkuk University Medical Center, Konkuk University School of Medicine, Seoul, South Korea
| | - Hyebin Lee
- Department of Radiation Oncology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, South Korea
- *Correspondence: Hyebin Lee, ; Han Suk Ryu,
| | - Han Suk Ryu
- Department of Pathology, Seoul National University College of Medicine, Seoul, South Korea
- Department of Pathology, Seoul National University Hospital, Seoul, South Korea
- Center for Medical Innovation, Biomedical Research Institute, Seoul National University Hospital, Seoul, South Korea
- *Correspondence: Hyebin Lee, ; Han Suk Ryu,
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Garrido-Casado M, Asensio-Juárez G, Vicente-Manzanares M. Nonmuscle Myosin II Regulation Directs Its Multiple Roles in Cell Migration and Division. Annu Rev Cell Dev Biol 2021; 37:285-310. [PMID: 34314591 DOI: 10.1146/annurev-cellbio-042721-105528] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nonmuscle myosin II (NMII) is a multimeric protein complex that generates most mechanical force in eukaryotic cells. NMII function is controlled at three main levels. The first level includes events that trigger conformational changes that extend the complex to enable its assembly into filaments. The second level controls the ATPase activity of the complex and its binding to microfilaments in extended NMII filaments. The third level includes events that modulate the stability and contractility of the filaments. They all work in concert to finely control force generation inside cells. NMII is a common endpoint of mechanochemical signaling pathways that control cellular responses to physical and chemical extracellular cues. Specific phosphorylations modulate NMII activation in a context-dependent manner. A few kinases control these phosphorylations in a spatially, temporally, and lineage-restricted fashion, enabling functional adaptability to the cellular microenvironment. Here, we review mechanisms that control NMII activity in the context of cell migration and division. Expected final online publication date for the Annual Review of Cell and Developmental Biology, Volume 37 is October 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Marina Garrido-Casado
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas, University of Salamanca, 37007 Salamanca, Spain;
| | - Gloria Asensio-Juárez
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas, University of Salamanca, 37007 Salamanca, Spain;
| | - Miguel Vicente-Manzanares
- Molecular Mechanisms Program, Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, Consejo Superior de Investigaciones Científicas, University of Salamanca, 37007 Salamanca, Spain;
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Hanicinec V, Brynychova V, Rosendorf J, Palek R, Liska V, Oliverius M, Kala Z, Mohelnikova-Duchonova B, Krus I, Soucek P. Gene expression of cytokinesis regulators PRC1, KIF14 and CIT has no prognostic role in colorectal and pancreatic cancer. Oncol Lett 2021; 22:598. [PMID: 34188700 PMCID: PMC8228381 DOI: 10.3892/ol.2021.12859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/12/2021] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer is one of the most common cancers and pancreatic cancer is among the most fatal and difficult to treat. New prognostic biomarkers are urgently needed to improve the treatment of colorectal and pancreatic cancer. Protein regulating cytokinesis 1 (PRC1), kinesin family member 14 (KIF14) and citron Rho-interacting serine/threonine kinase (CIT) serve important roles in cytokinesis, are strongly associated with cancer progression and have prognostic potential. The present study aimed to investigate the prognostic relevance of the PRC1, KIF14 and CIT genes in colorectal and pancreatic cancer. PRC1, KIF14 and CIT transcript expression was assessed by reverse transcription-quantitative PCR in tumors and paired distant unaffected mucosa from 67 patients with colorectal cancer and tumors and paired non-neoplastic control tissues from 48 patients with pancreatic cancer. The extent of transcript dysregulation between tumor and control tissues and between groups of patients divided by main clinical characteristics, namely patients' age and sex, disease stage, localization and grade, was determined. Finally, the associations of transcript levels in tumors with disease-free interval and overall survival time were evaluated. PRC1, KIF14 and CIT transcripts were upregulated in tumors compared with control tissues. PRC1, KIF14 and CIT levels strongly correlated to each other in both colorectal and pancreatic tumor and control tissues after correction for multiple testing. However, no significant associations were found among the transcript levels of PRC1, KIF14 and CIT and disease-free interval or overall survival time. In summary, the present study demonstrated mutual correlation of PRC1, KIF14 and CIT cytokinesis regulators with no clear prognostic value in pancreatic and colorectal cancers. Hence, according to the results of the present study, transcript levels of these genes cannot be clinically exploited as prognostic biomarkers in colorectal or pancreatic cancer patients.
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Affiliation(s)
- Vojtech Hanicinec
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic
| | - Veronika Brynychova
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic
| | - Jachym Rosendorf
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic.,Deparment of Surgery, Teaching Hospital and Faculty of Medicine in Pilsen, Charles University, 30460 Pilsen, Czech Republic
| | - Richard Palek
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic.,Deparment of Surgery, Teaching Hospital and Faculty of Medicine in Pilsen, Charles University, 30460 Pilsen, Czech Republic
| | - Vaclav Liska
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic.,Deparment of Surgery, Teaching Hospital and Faculty of Medicine in Pilsen, Charles University, 30460 Pilsen, Czech Republic
| | - Martin Oliverius
- Department of Surgery, Faculty Hospital Kralovske Vinohrady and Third Faculty of Medicine, Charles University, 10000 Prague, Czech Republic
| | - Zdenek Kala
- Department of Surgery, University Hospital Brno and Faculty of Medicine, Masaryk University, 62500 Brno, Czech Republic
| | - Beatrice Mohelnikova-Duchonova
- Department of Oncology and Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, 77900 Olomouc, Czech Republic
| | - Ivona Krus
- Department of Toxicogenomics, National Institute of Public Health, Prague 10042, Czech Republic
| | - Pavel Soucek
- Biomedical Centre, Faculty of Medicine in Pilsen, Charles University, 32300 Pilsen, Czech Republic.,Department of Toxicogenomics, National Institute of Public Health, Prague 10042, Czech Republic
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Choong WK, Sung TY. Somatic mutation subtypes of lung adenocarcinoma in East Asian reveal divergent biological characteristics and therapeutic vulnerabilities. iScience 2021; 24:102522. [PMID: 34142036 PMCID: PMC8188494 DOI: 10.1016/j.isci.2021.102522] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 03/25/2021] [Accepted: 05/04/2021] [Indexed: 12/25/2022] Open
Abstract
Lung adenocarcinoma (LUAD) patients in East Asia predominantly harbor oncogenic EGFR mutations. However, there remains a limited understanding of the biological characteristics and therapeutic vulnerabilities of the concurrent mutations of EGFR and other genes in LUAD. Here, we performed comprehensive bioinformatics analyses on 88 treatment-naïve East Asian LUAD patients. Based on somatic mutation clustering, we identified three somatic mutation subtypes: EGFR + TP53 co-mutation, EGFR mutation, and multiple-gene mutation. A proteogenomic analysis among subtypes revealed varying degrees of dysregulation in cell-cycle-related and immune-related processes. An immune-characteristic analysis revealed higher PDL1 protein expression in the EGFR + TP53 co-mutation subtype than in the EGFR mutation subtype, which may affect the therapeutic efficacy of anti-PD-L1 therapy. Moreover, integrating known and potential therapeutic target analysis reveals therapeutic vulnerabilities of specific subtypes and nominates candidate biomarkers for therapeutic intervention. This study provides new biological insight and therapeutic opportunities with respect to EGFR-mutant LUAD subtypes. Comprehensive clustering analysis reveals three somatic mutation subtypes Prognosis of EGFRmut/TP53mut subtype is worse than EGFRmut subtype EGFRmut/TP53mut subtype shows IFN signaling and antigen processing pathway signatures Proteome analysis identifies druggable proteins and candidates for drug repositioning
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Affiliation(s)
- Wai-Kok Choong
- Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan
| | - Ting-Yi Sung
- Institute of Information Science, Academia Sinica, Taipei, 115, Taiwan
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