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Lin H, Wang J, Shi Q, Wu M. Significance of NKX2-1 as a biomarker for clinical prognosis, immune infiltration, and drug therapy in lung squamous cell carcinoma. PeerJ 2024; 12:e17338. [PMID: 38708353 PMCID: PMC11069361 DOI: 10.7717/peerj.17338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 04/15/2024] [Indexed: 05/07/2024] Open
Abstract
Background This study was performed to determine the biological processes in which NKX2-1 is involved and thus its role in the development of lung squamous cell carcinoma (LUSC) toward improving the prognosis and treatment of LUSC. Methods Raw RNA sequencing (RNA-seq) data of LUSC from The Cancer Genome Atlas (TCGA) were used in bioinformatics analysis to characterize NKX2-1 expression levels in tumor and normal tissues. Survival analysis of Kaplan-Meier curve, the time-dependent receiver operating characteristic (ROC) curve, and a nomogram were used to analyze the prognosis value of NKX2-1 for LUSC in terms of overall survival (OS) and progression-free survival (PFS). Then, differentially expressed genes (DEGs) were identified, and Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), and Gene Set Enrichment Analysis (GSEA) were used to clarify the biological mechanisms potentially involved in the development of LUSC. Moreover, the correlation between the NKX2-1 expression level and tumor mutation burden (TMB), tumor microenvironment (TME), and immune cell infiltration revealed that NKX2-1 participates in the development of LUSC. Finally, we studied the effects of NKX2-1 on drug therapy. To validate the protein and gene expression levels of NKX2-1 in LUSC, we employed immunohistochemistry(IHC) datasets, The Gene Expression Omnibus (GEO) database, and qRT-PCR analysis. Results NKX2-1 expression levels were significantly lower in LUSC than in normal lung tissue. It significantly differed in gender, stage and N classification. The survival analysis revealed that high expression of NKX2-1 had shorter OS and PFS in LUSC. The multivariate Cox regression hazard model showed the NKX2-1 expression as an independent prognostic factor. Then, the nomogram predicted LUSC prognosis. There are 51 upregulated DEGs and 49 downregulated DEGs in the NKX2-1 high-level groups. GO, KEGG and GSEA analysis revealed that DEGs were enriched in cell cycle and DNA replication.The TME results show that NKX2-1 expression was positively associated with mast cells resting, neutrophils, monocytes, T cells CD4 memory resting, and M2 macrophages but negatively associated with M1 macrophages. The TMB correlated negatively with NKX2-1 expression. The pharmacotherapy had great sensitivity in the NKX2-1 low-level group, the immunotherapy is no significant difference in the NKX2-1 low-level and high-level groups. The analysis of GEO data demonstrated concurrence with TCGA results. IHC revealed NKX2-1 protein expression in tumor tissues of both LUAD and LUSC. Meanwhile qRT-PCR analysis indicated a significantly lower NKX2-1 expression level in LUSC compared to LUAD. These qRT-PCR findings were consistent with co-expression analysis of NKX2-1. Conclusion We conclude that NKX2-1 is a potential biomarker for prognosis and treatment LUSC. A new insights of NKX2-1 in LUSC is still needed further research.
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Affiliation(s)
- Huiyue Lin
- Oncology Department, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Juyong Wang
- Oncology Department, Longhua Hospital Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Qing Shi
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Minmin Wu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China
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Fukagawa K, Takahashi Y, Yamamichi N, Kageyama-Yahara N, Sakaguchi Y, Obata M, Cho R, Sakuma N, Nagao S, Miura Y, Tamura N, Ohki D, Mizutani H, Yakabi S, Minatsuki C, Niimi K, Tsuji Y, Yamamichi M, Shigi N, Tomida S, Abe H, Ushiku T, Koike K, Fujishiro M. Transcriptome analysis reveals the essential role of NK2 homeobox 1/thyroid transcription factor 1 ( NKX2-1/TTF-1) in gastric adenocarcinoma of fundic-gland type. Gastric Cancer 2023; 26:44-54. [PMID: 36094595 DOI: 10.1007/s10120-022-01334-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 08/17/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND Gastric adenocarcinoma of fundic-gland type (GA-FG) is a gastric malignancy with little relation to Helicobacter pylori. Clinical characteristics of GA-FG have been established, but molecular mechanisms leading to tumorigenesis have not yet been elucidated. METHODS We subjected three GA-FG tumors-normal mucosa pairs to microarray analysis. Network analysis was performed for the top 30 up-regulated gene transcripts, followed by immunohistochemical staining to confirm the gene expression analysis results. AGS and NUGC4 cells were transfected with the gene-encoding NK2 homeobox 1/thyroid transcription factor 1 (NKX2-1/TTF-1) to evaluate transcriptional changes in its target genes. RESULTS Comprehensive gene expression analysis identified 1410 up-regulated and 1395 down-regulated gene probes with ≥ two-fold difference in expression. Among the top 30 up-regulated genes in GA-FG, we identified transcription factor NKX2-1/TTF-1, a master regulator of lung/thyroid differentiation, together with surfactant protein B (SFTPB), SFTPC, and secretoglobin family 3A member 2(SCGB3A2), which are regulated by NKX2-1/TTF-1. Immunohistochemical analysis of 16 GA-FG specimens demonstrated significantly higher NKX2-1/TTF-1 and SFTPB levels, as compared to that in adjacent normal mucosa (P < 0.05), while SCGB3A2 levels did not differ (P = 0.341). Transduction of NKX2-1/TTF-1 into AGS and NUGC4 cells induced transactivation of SFTPB and SFTPC, indicating that NKX2-1/TTF-1 can function as normally in gastric cells as it can in the lung cells. CONCLUSIONS Our first transcriptome analysis of GA-FG indicates significant expression of NKX2-1/TTF1 in GA-FG. Immunohistochemistry and cell biology show ectopic expression and normal transactivation ability of NKX2-1/TTF-1, suggesting that it plays an essential role in GA-FG development.
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Affiliation(s)
- Kazushi Fukagawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Yu Takahashi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan.
| | - Nobutake Yamamichi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Natsuko Kageyama-Yahara
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Yoshiki Sakaguchi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Miho Obata
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Rina Cho
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Nobuyuki Sakuma
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Sayaka Nagao
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Yuko Miura
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Naoki Tamura
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Daisuke Ohki
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Hiroya Mizutani
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Seiichi Yakabi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Chihiro Minatsuki
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Keiko Niimi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Yosuke Tsuji
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Mitsue Yamamichi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Narumi Shigi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
| | - Shuta Tomida
- Center for Comprehensive Genomic Medicine, Okayama University Hospital, Okayama, Okayama, Japan
| | - Hiroyuki Abe
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Tetsuo Ushiku
- Department of Pathology, Graduate School of Medicine, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
- Kanto Central Hospital of the Mutual Aid Association of Public School Teachers, Setagaya-Ku, Tokyo, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, 7-3-1, Hongo, Bunkyo-Ku, Tokyo, 113-8655, Japan
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Kong R, Patel AS, Sato T, Jiang F, Yoo S, Bao L, Sinha A, Tian Y, Fridrikh M, Liu S, Feng J, He X, Jiang J, Ma Y, Grullon K, Yang D, Powell CA, Beasley MB, Zhu J, Snyder EL, Li S, Watanabe H. Transcriptional Circuitry of NKX2-1 and SOX1 Defines an Unrecognized Lineage Subtype of Small-Cell Lung Cancer. Am J Respir Crit Care Med 2022; 206:1480-1494. [PMID: 35848993 PMCID: PMC9757094 DOI: 10.1164/rccm.202110-2358oc] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 07/18/2022] [Indexed: 12/24/2022] Open
Abstract
Rationale: The current molecular classification of small-cell lung cancer (SCLC) on the basis of the expression of four lineage transcription factors still leaves its major subtype SCLC-A as a heterogeneous group, necessitating more precise characterization of lineage subclasses. Objectives: To refine the current SCLC classification with epigenomic profiles and to identify features of the redefined SCLC subtypes. Methods: We performed unsupervised clustering of epigenomic profiles on 25 SCLC cell lines. Functional significance of NKX2-1 (NK2 homeobox 1) was evaluated by cell growth, apoptosis, and xenograft using clustered regularly interspaced short palindromic repeats-Cas9 (CRISPR-associated protein 9)-mediated deletion. NKX2-1-specific cistromic profiles were determined using chromatin immunoprecipitation followed by sequencing, and its functional transcriptional partners were determined using coimmunoprecipitation followed by mass spectrometry. Rb1flox/flox; Trp53flox/flox and Rb1flox/flox; Trp53flox/flox; Nkx2-1flox/flox mouse models were engineered to explore the function of Nkx2-1 in SCLC tumorigenesis. Epigenomic landscapes of six human SCLC specimens and 20 tumors from two mouse models were characterized. Measurements and Main Results: We identified two epigenomic subclusters of the major SCLC-A subtype: SCLC-Aα and SCLC-Aσ. SCLC-Aα was characterized by the presence of a super-enhancer at the NKX2-1 locus, which was observed in human SCLC specimens and a murine SCLC model. We found that NKX2-1, a dual lung and neural lineage factor, is uniquely relevant in SCLC-Aα. In addition, we found that maintenance of this neural identity in SCLC-Aα is mediated by collaborative transcriptional activity with another neuronal transcriptional factor, SOX1 (SRY-box transcription factor 1). Conclusions: We comprehensively describe additional epigenomic heterogeneity of the major SCLC-A subtype and define the SCLC-Aα subtype by the core regulatory circuitry of NKX2-1 and SOX1 super-enhancers and their functional collaborations to maintain neuronal linage state.
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Affiliation(s)
- Ranran Kong
- Department of Thoracic Surgery and
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Ayushi S. Patel
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
- Division of Hematology and Medical Oncology, Laura and Isaac Perlmutter Cancer Center, Langone Medical Center, New York University, New York, New York
| | - Takashi Sato
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
- Department of Respiratory Medicine, School of Medicine, Kitasato University, Sagamihara, Japan
- Division of Pulmonary Medicine, Department of Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Feng Jiang
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Seungyeul Yoo
- Department of Genetics and Genomic Sciences, and
- Sema4, Stamford, Connecticut
| | - Li Bao
- People’s Hospital of Ningxia Hui Autonomous Region, Yinchuan, China
| | - Abhilasha Sinha
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Yang Tian
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Maya Fridrikh
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Shuhui Liu
- Division of Infectious Diseases, Department of Medicine
| | - Jie Feng
- Department of Nephrology, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
| | - Xijing He
- Department of Orthopedics, The Second Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- Xi’an International Medical Center, Xi’an, China
| | | | | | - Karina Grullon
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Dawei Yang
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital Fudan University, Shanghai, China; and
| | - Charles A. Powell
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
| | - Mary Beth Beasley
- Department of Pathology and Laboratory Medicine, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jun Zhu
- Tisch Cancer Institute
- Department of Genetics and Genomic Sciences, and
- Sema4, Stamford, Connecticut
| | - Eric L. Snyder
- Department of Pathology
- Department of Oncological Sciences, and
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | | | - Hideo Watanabe
- Division of Pulmonary, Critical Care and Sleep Medicine
- Tisch Cancer Institute
- Department of Genetics and Genomic Sciences, and
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