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Yu Y, Liu M, Wang Z, Liu Y, Yao M, Wang L, Zhong L. Identification of oxidative stress signatures of lung adenocarcinoma and prediction of patient prognosis or treatment response with single-cell RNA sequencing and bulk RNA sequencing data. Int Immunopharmacol 2024; 137:112495. [PMID: 38901238 DOI: 10.1016/j.intimp.2024.112495] [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: 01/24/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024]
Abstract
Lung adenocarcinoma (LUAD), the most common subtype of lung cancer globally, has seen improved prognosis with advancements in diagnostic, surgical, radiotherapy, and molecular therapy techniques, while its 5-year survival rate remains low. Molecular biomarkers provide prognostic value. Oxidative stress factors, such as reactive nitrogen species and ROS, are crucial in various stages of tumor progression, influencing cell transformation, proliferation, angiogenesis, and metastasis. ROS demonstrate dual roles, affecting tumor cells, hypoxia sensitivity, and the microenvironment. Comprehensive analysis of oxidative stress in LUAD has not been conducted to date. Therefore, we systematically investigated the regulatory patterns of oxidative stress in LUAD based on oxidative stress-related genes and correlated these patterns with cellular infiltration characteristics of the tumor immune microenvironment. The model utilizes single-factor Cox analysis to screen key differential genes with prognostic value and employs least absolute shrinkage and selection operator (LASSO) penalized Cox regression analysis to construct a prognostic-related prediction model. Ten candidate genes were selected based on this model. The risk score was constructed using the coefficients and expression levels of these ten genes. Furthermore, the impact of this risk score on overall survival (OS) was determined. Two genes with the most significant differential expression, SFTPB and S100P, were selected through qRT-PCR. Cell experiments including CCK-8, Edu, transwell assays confirmed their effects on lung cancer cells growth, consistent with the results of bioinformatics analysis. These findings suggested that this model held potential clinical value for evaluating the prognosis of lung adenocarcinoma.
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Affiliation(s)
- Yunchi Yu
- Department of Thoracic Surgery and Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, Jiangsu, China
| | - Miaoyan Liu
- Department of Thoracic Surgery and Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, Jiangsu, China
| | - Zihang Wang
- Department of Thoracic Surgery and Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, Jiangsu, China
| | - Yufan Liu
- Department of Thoracic Surgery and Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, Jiangsu, China
| | - Min Yao
- Department of Thoracic Surgery and Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, Jiangsu, China
| | - Li Wang
- Research Center for Intelligence Information Technology, Nantong University, Nantong 226001, Jiangsu, China
| | - Lou Zhong
- Department of Thoracic Surgery and Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong 226001, Jiangsu, China.
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2
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Pulice JL, Meyerson M. Dosage amplification dictates oncogenic regulation by the NKX2-1 lineage factor in lung adenocarcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.26.563996. [PMID: 37994369 PMCID: PMC10664179 DOI: 10.1101/2023.10.26.563996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
Amplified oncogene expression is a critical and widespread driver event in cancer, yet our understanding of how amplification-mediated elevated dosage mediates oncogenic regulation is limited. Here, we find that the most significant focal amplification event in lung adenocarcinoma (LUAD) targets a lineage super-enhancer near the NKX2-1 lineage transcription factor. The NKX2-1 super-enhancer is targeted by focal and co-amplification with NKX2-1, and activation or repression controls NKX2-1 expression. We find that NKX2-1 is a widespread dependency in LUAD cell lines, where NKX2-1 pioneers enhancer accessibility to drive a lineage addicted state in LUAD, and NKX2-1 confers persistence to EGFR inhibitors. Notably, we find that oncogenic NKX2-1 regulation requires expression above a minimum dosage threshold-NKX2-1 dosage below this threshold is insufficient for cell viability, enhancer remodeling, and TKI persistence. Our data suggest that copy-number amplification can be a gain-of-function alteration, wherein amplification elevates oncogene expression above a critical dosage required for oncogenic regulation and cancer cell survival.
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Affiliation(s)
- John L. Pulice
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Biological and Biomedical Sciences Program, Harvard University, Cambridge, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Lead contact
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3
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Tomoshige K, Stuart WD, Fink-Baldauf IM, Ito M, Tsuchiya T, Nagayasu T, Yamatsuji T, Okada M, Fukazawa T, Guo M, Maeda Y. FOXA2 Cooperates with Mutant KRAS to Drive Invasive Mucinous Adenocarcinoma of the Lung. Cancer Res 2023; 83:1443-1458. [PMID: 37067057 PMCID: PMC10160002 DOI: 10.1158/0008-5472.can-22-2805] [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: 09/04/2022] [Revised: 01/04/2023] [Accepted: 02/24/2023] [Indexed: 04/18/2023]
Abstract
The endoderm-lineage transcription factor FOXA2 has been shown to inhibit lung tumorigenesis in in vitro and xenograft studies using lung cancer cell lines. However, FOXA2 expression in primary lung tumors does not correlate with an improved patient survival rate, and the functional role of FOXA2 in primary lung tumors remains elusive. To understand the role of FOXA2 in primary lung tumors in vivo, here, we conditionally induced the expression of FOXA2 along with either of the two major lung cancer oncogenes, EGFRL858R or KRASG12D, in the lung epithelium of transgenic mice. Notably, FOXA2 suppressed autochthonous lung tumor development driven by EGFRL858R, whereas FOXA2 promoted tumor growth driven by KRASG12D. Importantly, FOXA2 expression along with KRASG12D produced invasive mucinous adenocarcinoma (IMA) of the lung, a fatal mucus-producing lung cancer comprising approximately 5% of human lung cancer cases. In the mouse model in vivo and human lung cancer cells in vitro, FOXA2 activated a gene regulatory network involved in the key mucous transcription factor SPDEF and upregulated MUC5AC, whose expression is critical for inducing IMA. Coexpression of FOXA2 with mutant KRAS synergistically induced MUC5AC expression compared with that induced by FOXA2 alone. ChIP-seq combined with CRISPR interference indicated that FOXA2 bound directly to the enhancer region of MUC5AC and induced the H3K27ac enhancer mark. Furthermore, FOXA2 was found to be highly expressed in primary tumors of human IMA. Collectively, this study reveals that FOXA2 is not only a biomarker but also a driver for IMA in the presence of a KRAS mutation. SIGNIFICANCE FOXA2 expression combined with mutant KRAS drives invasive mucinous adenocarcinoma of the lung by synergistically promoting a mucous transcriptional program, suggesting strategies for targeting this lung cancer type that lacks effective therapies.
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Affiliation(s)
- Koichi Tomoshige
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - William D. Stuart
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Iris M. Fink-Baldauf
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Masaoki Ito
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Tomoshi Tsuchiya
- Department of Surgical Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Takeshi Nagayasu
- Department of Surgical Oncology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Tomoki Yamatsuji
- Department of General Surgery, Kawasaki Medical School, Okayama, Japan
| | - Morihito Okada
- Department of Surgical Oncology, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Japan
| | - Takuya Fukazawa
- Department of General Surgery, Kawasaki Medical School, Okayama, Japan
| | - Minzhe Guo
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yutaka Maeda
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children’s Hospital Medical Center and the University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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4
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Gloriane C Luna H, Severino Imasa M, Juat N, Hernandez KV, May Sayo T, Cristal-Luna G, Marie Asur-Galang S, Bellengan M, John Duga K, Brian Buenaobra B, De Los Santos MI, Medina D, Samo J, Minerva Literal V, Andrew Bascos N, Sy-Naval S. Expression landscapes in non-small cell lung cancer shaped by the thyroid transcription factor 1. Lung Cancer 2023; 176:121-131. [PMID: 36634573 DOI: 10.1016/j.lungcan.2022.12.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 12/20/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022]
Abstract
TTF-1-expressing non-small cell lung cancer (NSCLC) is one of the most prevalent lung cancer types worldwide. However, theparadoxical activity of TTF-1 in both lung carcinogenesis and tumor suppression is believed to be context-dependentwhich calls for a deeper understanding about the pathological expression of TTF-1. In addition, the expression circuitry of TTF-1-target genes in NSCLC has not been well examined which necessitates to revisit the involvement of TTF-1- in a multitude of oncologic pathways. We used RNA-seq and clinical data of patients from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx), including ChIP-seq data from different NSCLC cell lines, and mapped the proteome of NSCLC tumor. Our analysis showed significant variability in TTF-1 expression among NSCLC,and further clarified that this variability is orchestrated at the transcriptional level. We also found that high TTF-1 expression could negatively influence the survival outcomes of stage 1 LUAD which may be attributed to growth factor receptor-driven activation of mitogenic and angiogenic pathways. Mechanistically, TTF-1 may also control the genes associated with pathways involved in acquired TKI drug resistance or response to immune checkpoint inhibitors. Lastly, proteome-based biomarker discovery in stage 1 LUAD showed that TTF-1 positivity is potentially associated with the upregulation of several oncogenes which includes interferon proteins, MUC1, STAT3, and EIF2AK2. Collectively, this study highlights the potential involvement of TTF-1 in cell proliferation, immune evasion, and angiogenesis in early-stage NSCLC.
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Affiliation(s)
- Herdee Gloriane C Luna
- Department of Internal Medicine, Lung Center of the Philippines, Quezon Ave, Diliman, Quezon City, Metro Manila 1100, Philippines; Department of Internal Medicine, National Kidney and Transplant Institute, East Avenue, Diliman, Quezon City 1101, Philippines.
| | - Marcelo Severino Imasa
- Department of Internal Medicine, Lung Center of the Philippines, Quezon Ave, Diliman, Quezon City, Metro Manila 1100, Philippines
| | - Necy Juat
- Department of Internal Medicine, National Kidney and Transplant Institute, East Avenue, Diliman, Quezon City 1101, Philippines
| | - Katherine V Hernandez
- Department of Internal Medicine, East Avenue Medical Center, East Ave, Diliman, Quezon City, Metro Manila 1100, Philippines
| | - Treah May Sayo
- Department of Internal Pathology, Lung Center of the Philippines, Quezon Ave, Diliman, Quezon City, Metro Manila 1100, Philippines
| | - Gloria Cristal-Luna
- Department of Internal Medicine, National Kidney and Transplant Institute, East Avenue, Diliman, Quezon City 1101, Philippines
| | - Sheena Marie Asur-Galang
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology, Philippine Council for Health Research and Development, Philippines
| | - Mirasol Bellengan
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology, Philippine Council for Health Research and Development, Philippines
| | - Kent John Duga
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology, Philippine Council for Health Research and Development, Philippines
| | - Bien Brian Buenaobra
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology, Philippine Council for Health Research and Development, Philippines
| | - Marvin I De Los Santos
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology, Philippine Council for Health Research and Development, Philippines
| | - Daniel Medina
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology, Philippine Council for Health Research and Development, Philippines
| | - Jamirah Samo
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology, Philippine Council for Health Research and Development, Philippines
| | - Venus Minerva Literal
- Clinical Proteomics for Cancer Initiative, Department of Science and Technology, Philippine Council for Health Research and Development, Philippines
| | - Neil Andrew Bascos
- National Institute of Molecular Biology and Biotechnology, University of the Philippines - Diliman, Diliman, Quezon City, Metro Manila, Philippines; Protein, Proteomics and Metabolomics Facility, Philippine Genome Center, University of the Philippines System, Philippines
| | - Sullian Sy-Naval
- Department of Internal Medicine, Lung Center of the Philippines, Quezon Ave, Diliman, Quezon City, Metro Manila 1100, Philippines
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5
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Zhao L, Li M, Yin Z, Lv L, Zhou M, Wang Y, Zhang M, Guo T, Guo X, Liu H, Cheng L, Liang X, Duo S, Li R. Development of a Lung Vacancy Mouse Model through CRISPR/Cas9-Mediated Deletion of Thyroid Transcription Factor 1 Exon 2. Cells 2022; 11:cells11233874. [PMID: 36497134 PMCID: PMC9740088 DOI: 10.3390/cells11233874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/28/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
A developmental niche vacancy in host embryos is necessary for stem cell complementation-based organ regeneration (SCOG). Thyroid transcription factor 1 (TTF-1) is a tissue-specific transcription factor that regulates the embryonic development and differentiation of the thyroid and, more importantly, lungs; thus, it has been considered as a master gene to knockout in order to develop a lung vacancy host. TTF-1 knockout mice were originally produced by inserting a stop codon in Exon 3 of the gene (E3stop) through embryonic stem cell-based homologous recombination. The main problems of utilizing E3stop host embryos for lung SCOG are that these animals all have a tracheoesophageal fistula (TEF), which cannot be corrected by donor stem cells, and most of them have monolateral sac-like lungs. To improve the mouse model towards achieving SCOG-based lung generation, in this project, we used the CRISPR/Cas9 tool to remove Exon 2 of the gene by zygote microinjection and successfully produced TTF-1 knockout (E2del) mice. Similar to E3stop, E2del mice are birth-lethal due to retarded lung development with sac-like lungs and only a rudimentary bronchial tree, increased basal cells but without alveolar type II cells and blood vessels, and abnormal thyroid development. Unlike E3stop, 57% of the E2del embryos presented type I tracheal agenesis (TA, a kind of human congenital malformation) with a shortened trachea and clear separations of the trachea and esophagus, while the remaining 43% had TEF. Furthermore, all the E2del mice had bilateral sac-like lungs. Both TA and bilateral sac-like lungs are preferred in SCOG. Our work presents a new strategy for producing SCOG host embryos that may be useful for lung regeneration.
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Affiliation(s)
- Lihua Zhao
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
| | - Meishuang Li
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China
| | - Zhibao Yin
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China
| | - Limin Lv
- Laboratory Animal Center, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Meng Zhou
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China
| | - Yixi Wang
- Laboratory Animal Center, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Manling Zhang
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China
| | - Tianxu Guo
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China
| | - Xiyun Guo
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China
| | - Han Liu
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China
| | - Linxin Cheng
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China
| | - Xiubin Liang
- Department of Pathophysiology, Nanjing Medical University, Nanjing 211166, China
| | - Shuguang Duo
- Laboratory Animal Center, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Correspondence: (S.D.); (R.L.)
| | - Rongfeng Li
- Jiangsu Key Laboratory of Xenotransplantation, Nanjing Medical University, Nanjing 211166, China
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing 211166, China
- Correspondence: (S.D.); (R.L.)
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6
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Mills C, Riching A, Keller A, Stombaugh J, Haupt A, Maksimova E, Dickerson SM, Anderson E, Hemphill K, Ebmeier C, Schiel JA, Levenga J, Perkett M, Smith AVB, Strezoska Z. A Novel CRISPR Interference Effector Enabling Functional Gene Characterization with Synthetic Guide RNAs. CRISPR J 2022; 5:769-786. [PMID: 36257604 PMCID: PMC9805873 DOI: 10.1089/crispr.2022.0056] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/15/2022] [Indexed: 01/31/2023] Open
Abstract
While CRISPR interference (CRISPRi) systems have been widely implemented in pooled lentiviral screening, there has been limited use with synthetic guide RNAs for the complex phenotypic readouts enabled by experiments in arrayed format. Here we describe a novel deactivated Cas9 fusion protein, dCas9-SALL1-SDS3, which produces greater target gene repression than first or second generation CRISPRi systems when used with chemically modified synthetic single guide RNAs (sgRNAs), while exhibiting high target specificity. We show that dCas9-SALL1-SDS3 interacts with key members of the histone deacetylase and Swi-independent three complexes, which are the endogenous functional effectors of SALL1 and SDS3. Synthetic sgRNAs can also be used with in vitro-transcribed dCas9-SALL1-SDS3 mRNA for short-term delivery into primary cells, including human induced pluripotent stem cells and primary T cells. Finally, we used dCas9-SALL1-SDS3 for functional gene characterization of DNA damage host factors, orthogonally to small interfering RNA, demonstrating the ability of the system to be used in arrayed-format screening.
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Affiliation(s)
- Clarence Mills
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Andrew Riching
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Ashleigh Keller
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Jesse Stombaugh
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Amanda Haupt
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Elena Maksimova
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Sarah M. Dickerson
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Emily Anderson
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Kevin Hemphill
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Chris Ebmeier
- Mass Spectrometry Core Facility, University of Colorado-Boulder, Boulder, Colorado, USA
| | - John A. Schiel
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Josien Levenga
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Matthew Perkett
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Anja van Brabant Smith
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
| | - Zaklina Strezoska
- Horizon Discovery, a PerkinElmer Company, Lafayette, Colorado, USA and University of Colorado-Boulder, Boulder, Colorado, USA
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7
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Tansathitaya V, Sarasin W, Phakham T, Sawaswong V, Chanchaem P, Payungporn S. Regulation of mi-RNAs Target Cancer Genes Between Exercise and Non-exercise in Rat Rheumatoid Arthritis Induction: Pilot Study. Epigenet Insights 2022; 15:25168657221110485. [PMID: 35800470 PMCID: PMC9253985 DOI: 10.1177/25168657221110485] [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: 03/18/2022] [Accepted: 06/13/2022] [Indexed: 12/13/2022] Open
Abstract
Introduction: Rheumatoid arthritis is associated with various cancers. Many studies have
investigated physical exercise interventions as health improvements to
ameliorate the risk of cancer during rheumatoid arthritis diagnosis.
Recently, microRNAs were used as biomarkers for health assessment and cancer
prediction in rheumatoid arthritis patients. Methods: The effects of exercise interventions on serum microRNAs were investigated in
pristane-induced arthritis (PIA) rat models. Twelve Sprague-Dawley male rats
were divided into 4 groups including non-exercise without PIA (N-EX),
non-exercise with PIA (N-EX + PIA), exercise without PIA (EX) and exercise
with PIA (EX + PIA). Blood samples were collected at the end of the study
period to analyze miRNA biomarkers and target cancer gene predictions. Results: Four significant Rattus norvegicus (rno-microRNAs) may purpose as tumor
suppressors were identified as potential target cancer gene candidate
expressions within the 4 comparative interventional exercise groups. One
rno-microRNA and target cancer gene candidate was up-regulated and 3
rno-microRNAs and their target cancer genes were down-regulated. Conclusions: Exercise interventions affected rno-miRNAs regulated target cancer gene
candidates ITPR3, SOCS6, ITGA6, and NKX2-1 as biomarkers for cancer
prognosis in rheumatoid arthritis diagnosis.
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Affiliation(s)
- Vimolmas Tansathitaya
- College of Sports Science and Technology, Mahidol University, Nakhon Pathom, Thailand
| | - Witchana Sarasin
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tanapati Phakham
- Center of Excellence in Systems Biology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Vorthon Sawaswong
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Prangwalai Chanchaem
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Sunchai Payungporn
- Research Unit of Systems Microbiology, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
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8
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Fink-Baldauf IM, Stuart WD, Brewington JJ, Guo M, Maeda Y. CRISPRi links COVID-19 GWAS loci to LZTFL1 and RAVER1. EBioMedicine 2022; 75:103806. [PMID: 34998241 PMCID: PMC8731227 DOI: 10.1016/j.ebiom.2021.103806] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 01/08/2023] Open
Abstract
Background To identify host genetic variants (SNPs) associated with COVID-19 disease severity, a number of genome-wide association studies (GWAS) have been conducted. Since most of the identified variants are located at non-coding regions, such variants are presumed to affect the expression of neighbouring genes, thereby influencing COVID-19 disease severity. However, it remains largely unknown which genes are influenced by such COVID-19 GWAS loci. Methods CRISPRi (interference)-mediated gene expression analysis was performed to identify genes functionally regulated by COVID-19 GWAS loci by targeting regions near the loci (SNPs) in lung epithelial cell lines. The expression of CRISPRi-identified genes was investigated using COVID-19-contracted human and monkey lung single-nucleus/cell (sn/sc) RNA-seq datasets. Findings CRISPRi analysis indicated that a region near rs11385942 at chromosome 3p21.31 (locus of highest significance with COVID-19 disease severity at intron 5 of LZTFL1) significantly affected the expression of LZTFL1 (P<0.05), an airway cilia regulator. A region near rs74956615 at chromosome 19p13.2 (locus located at the 3’ untranslated exonic region of RAVER1), which is associated with critical illness in COVID-19, affected the expression of RAVER1 (P<0.05), a coactivator of MDA5 (IFIH1), which induces antiviral response genes, including ICAM1. The sn/scRNA-seq datasets indicated that the MDA5/RAVER1-ICAM1 pathway was activated in lung epithelial cells of COVID-19-resistant monkeys but not those of COVID-19-succumbed humans. Interpretation Patients with risk alleles of rs11385942 and rs74956615 may be susceptible to critical illness in COVID-19 in part through weakened airway viral clearance via LZTFL1-mediated ciliogenesis and diminished antiviral immune response via the MDA5/RAVER1 pathway, respectively. Funding NIH.
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MESH Headings
- Animals
- COVID-19/genetics
- COVID-19/metabolism
- CRISPR-Cas Systems
- Chromosomes, Human, Pair 19/genetics
- Chromosomes, Human, Pair 19/metabolism
- Chromosomes, Human, Pair 3/genetics
- Chromosomes, Human, Pair 3/metabolism
- Databases, Nucleic Acid
- Genetic Loci
- Genome-Wide Association Study
- Haplorhini
- Humans
- Polymorphism, Single Nucleotide
- RNA-Seq
- Ribonucleoproteins/genetics
- Ribonucleoproteins/metabolism
- SARS-CoV-2/genetics
- SARS-CoV-2/metabolism
- Transcription Factors/genetics
- Transcription Factors/metabolism
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Affiliation(s)
- Iris M Fink-Baldauf
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine (CCHMC and UC), Cincinnati, OH, USA
| | - William D Stuart
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine (CCHMC and UC), Cincinnati, OH, USA
| | - John J Brewington
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine (CCHMC and UC), Cincinnati, OH, USA
| | - Minzhe Guo
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine (CCHMC and UC), Cincinnati, OH, USA
| | - Yutaka Maeda
- Perinatal Institute, Division of Neonatology, Perinatal and Pulmonary Biology, Cincinnati Children's Hospital Medical Center and Department of Pediatrics, University of Cincinnati College of Medicine (CCHMC and UC), Cincinnati, OH, USA.
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Feng J, Han X, Yuan Y, Cho CK, Janečková E, Guo T, Pareek S, Rahman MS, Zheng B, Bi J, Jing J, Zhang M, Xu J, Ho TV, Chai Y. TGF-β signaling and Creb5 cooperatively regulate Fgf18 to control pharyngeal muscle development. eLife 2022; 11:80405. [PMID: 36542062 PMCID: PMC9771365 DOI: 10.7554/elife.80405] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
The communication between myogenic cells and their surrounding connective tissues is indispensable for muscle morphogenesis. During late embryonic development in mice, myogenic progenitors migrate to discrete sites to form individual muscles. The detailed mechanism of this process remains unclear. Using mouse levator veli palatini (LVP) development as a model, we systematically investigated how a distinct connective tissue subpopulation, perimysial fibroblasts, communicates with myogenic cells to regulate mouse pharyngeal myogenesis. Using single-cell RNAseq data analysis, we identified that TGF-β signaling is a key regulator for the perimysial fibroblasts. Loss of TGF-β signaling in the neural crest-derived palatal mesenchyme leads to defects in perimysial fibroblasts and muscle malformation in the soft palate in Osr2Cre;Tgfbr1fl/fl mice. In particular, Creb5, a transcription factor expressed in the perimysial fibroblasts, cooperates with TGF-β signaling to activate expression of Fgf18. Moreover, Fgf18 supports pharyngeal muscle development in vivo and exogenous Fgf18 can partially rescue myogenic cell numbers in Osr2Cre;Tgfbr1fl/fl samples, illustrating that TGF-β-regulated Fgf18 signaling is required for LVP development. Collectively, our findings reveal the mechanism by which TGF-β signaling achieves its functional specificity in defining the perimysial-to-myogenic signals for pharyngeal myogenesis.
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Affiliation(s)
- Jifan Feng
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Xia Han
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Yuan Yuan
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Courtney Kyeong Cho
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Eva Janečková
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Tingwei Guo
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Siddhika Pareek
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Md Shaifur Rahman
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Banghong Zheng
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Jing Bi
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Junjun Jing
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Mingyi Zhang
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Jian Xu
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Thach-Vu Ho
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
| | - Yang Chai
- Center for Craniofacial Molecular Biology, University of Southern CaliforniaLos AngelesUnited States
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Floros J, Tsotakos N. Differential Regulation of Human Surfactant Protein A Genes, SFTPA1 and SFTPA2, and Their Corresponding Variants. Front Immunol 2021; 12:766719. [PMID: 34917085 PMCID: PMC8669794 DOI: 10.3389/fimmu.2021.766719] [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: 08/29/2021] [Accepted: 11/02/2021] [Indexed: 11/26/2022] Open
Abstract
The human SFTPA1 and SFTPA2 genes encode the surfactant protein A1 (SP-A1) and SP-A2, respectively, and they have been identified with significant genetic and epigenetic variability including sequence, deletion/insertions, and splice variants. The surfactant proteins, SP-A1 and SP-A2, and their corresponding variants play important roles in several processes of innate immunity as well in surfactant-related functions as reviewed elsewhere [1]. The levels of SP-A have been shown to differ among individuals both under baseline conditions and in response to various agents or disease states. Moreover, a number of agents have been shown to differentially regulate SFTPA1 and SFTPA2 transcripts. The focus in this review is on the differential regulation of SFTPA1 and SFTPA2 with primary focus on the role of 5′ and 3′ untranslated regions (UTRs) and flanking sequences on this differential regulation as well molecules that may mediate the differential regulation.
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Affiliation(s)
- Joanna Floros
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, United States.,Department of Obstetrics and Gynecology, The Pennsylvania State University College of Medicine, Hershey, PA, United States
| | - Nikolaos Tsotakos
- School of Science, Engineering, and Technology, The Pennsylvania State University - Harrisburg, Middletown, PA, United States
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