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Rawal CC, Loubiere V, Butova NL, Gracia J, Parreno V, Merigliano C, Martinez AM, Cavalli G, Chiolo I. Sustained inactivation of the Polycomb PRC1 complex induces DNA repair defects and genomic instability in epigenetic tumors. Histochem Cell Biol 2024; 162:133-147. [PMID: 38888809 PMCID: PMC11227471 DOI: 10.1007/s00418-024-02302-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2024] [Indexed: 06/20/2024]
Abstract
Cancer initiation and progression are typically associated with the accumulation of driver mutations and genomic instability. However, recent studies demonstrated that cancer can also be driven purely by epigenetic alterations, without driver mutations. Specifically, a 24-h transient downregulation of polyhomeotic (ph-KD), a core component of the Polycomb complex PRC1, is sufficient to induce epigenetically initiated cancers (EICs) in Drosophila, which are proficient in DNA repair and characterized by a stable genome. Whether genomic instability eventually occurs when PRC1 downregulation is performed for extended periods of time remains unclear. Here, we show that prolonged depletion of PH, which mimics cancer initiating events, results in broad dysregulation of DNA replication and repair genes, along with the accumulation of DNA breaks, defective repair, and widespread genomic instability in the cancer tissue. A broad misregulation of H2AK118 ubiquitylation and to a lesser extent of H3K27 trimethylation also occurs and might contribute to these phenotypes. Together, this study supports a model where DNA repair and replication defects accumulate during the tumorigenic transformation epigenetically induced by PRC1 loss, resulting in genomic instability and cancer progression.
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Affiliation(s)
- Chetan C Rawal
- Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Vincent Loubiere
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - Nadejda L Butova
- Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Juliette Gracia
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - Victoria Parreno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - Chiara Merigliano
- Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA
| | - Anne-Marie Martinez
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
| | - Irene Chiolo
- Department of Molecular and Computational Biology, University of Southern California, 1050 Childs Way, Los Angeles, CA, 90089, USA.
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Rawal CC, Loubiere V, Butova NL, Garcia J, Parreno V, Martinez AM, Cavalli G, Chiolo I. Sustained inactivation of the Polycomb PRC1 complex induces DNA repair defects and genomic instability in epigenetic tumors. RESEARCH SQUARE 2024:rs.3.rs-4289524. [PMID: 38746379 PMCID: PMC11092839 DOI: 10.21203/rs.3.rs-4289524/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Cancer initiation and progression are typically associated with the accumulation of driver mutations and genomic instability. However, recent studies demonstrated that cancers can also be purely initiated by epigenetic alterations, without driver mutations. Specifically, a 24-hours transient down-regulation of polyhomeotic (ph-KD), a core component of the Polycomb complex PRC1, is sufficient to drive epigenetically initiated cancers (EICs) in Drosophila, which are proficient in DNA repair and are characterized by a stable genome. Whether genomic instability eventually occurs when PRC1 down-regulation is performed for extended periods of time remains unclear. Here we show that prolonged depletion of a PRC1 component, which mimics cancer initiating events, results in broad dysregulation of DNA replication and repair genes, along with the accumulation of DNA breaks, defective repair, and widespread genomic instability in the cancer tissue. A broad mis-regulation of H2AK118 ubiquitylation and to a lesser extent of H3K27 trimethylation also occurs, and might contribute to these phenotypes. Together, this study supports a model where DNA repair and replication defects amplify the tumorigenic transformation epigenetically induced by PRC1 loss, resulting in genomic instability and cancer progression.
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Wang K, Chu Y, Zhang H, Qu X, Wang B, Han Y. FOXD3 Suppresses the Proliferation of CRC Bone Metastatic Cells via the Ras/Raf/MEK/ERK Signaling Pathway. Comb Chem High Throughput Screen 2024; 27:436-445. [PMID: 37151068 PMCID: PMC10964126 DOI: 10.2174/1386207326666230505111008] [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: 10/01/2022] [Revised: 03/21/2023] [Accepted: 03/29/2023] [Indexed: 05/09/2023]
Abstract
BACKGROUND The improvements in the treatment of colorectal cancer (CRC) and prolongation of survival time have improved the incidence of bone metastasis. Forkhead box D3 (FOXD3) is involved in the development of CRC. However, the role and mechanism of FOXD3 in CRC bone metastases development are unknown. OBJECTIVE Using the combined bioinformatics and cytology experimental analyses, this study aimed to explore the mechanistic role of FOXD3 in the bone metastasis of colon cancer, thereby aiding in the treatment of colon cancer bone metastasis and identification of drug-targeting markers. METHODS First, the changes in the expression levels of the FOXD3 gene and differentially expressed genes (DEGs) between the colon cancer samples and colon cancer metastases were obtained from The Cancer Genome Atlas (TCGA) database. Then, the correlations of the FOXD3 gene with the DEGs were identified. Next, the effects of the FOXD3 on the proliferation and invasion abilities of colon cancer bone metastatic cells were identified using Cell Counting Kit-8 (CCK8) and Transwell cell migration assays, respectively. In addition, Western blot analysis was used to identify the expression levels of the proteins related to the EGFR/Ras/Raf/MEK/ERK (EGFR/ERK) signaling pathway and epithelial-to-mesenchymal transition (EMT). RESULTS FOXD3 was downregulated in colon cancer and could interact with multiple DEGs in colon cancer bone metastases. FOXD3 gene knockdown could increase the proliferation of human colon cancer bone metastatic cells and their invasive ability. FOXD3 gene knockdown could activate the expression of EGFR/ERK signaling pathway-related proteins and inhibit/promote the expression of EMT-related proteins, which in turn promoted the proliferation and metastasis of LoVo cells from colon cancer bone metastases. CONCLUSION Overall, this study demonstrated that the downregulation of the FOXD3 gene might promote the proliferation of colon cancer bone metastatic cell lines through the EGFR/ERK pathway and promote their migration through EMT, thereby serving as a promising therapeutic target.
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Affiliation(s)
- Kangwei Wang
- Department of Oncological Surgery, Minhang Branch, Cancer Hospital, Fudan University, Shanghai, China
| | - Yan Chu
- Shanghai Fifth People's Hospital, Fudan University, Shanghai, China
| | - Hongqiang Zhang
- Department of Oncological Surgery, Minhang Branch, Cancer Hospital, Fudan University, Shanghai, China
| | - Xinglong Qu
- Department of Oncological Surgery, Minhang Branch, Cancer Hospital, Fudan University, Shanghai, China
| | - Bing Wang
- Department of Oncological Surgery, Minhang Branch, Cancer Hospital, Fudan University, Shanghai, China
| | - Yu Han
- Department of Oncological Surgery, Minhang Branch, Cancer Hospital, Fudan University, Shanghai, China
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Mubeen A, Parra-Herran C. FOXL2: a gene central to ovarian function. J Clin Pathol 2023; 76:798-801. [PMID: 37798106 DOI: 10.1136/jcp-2023-208827] [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] [Accepted: 09/06/2023] [Indexed: 10/07/2023]
Abstract
The FOXL2 (forkhead box L2) gene is located on chromosome 3 and encodes for forkhead box (FOX) family of transcription factors which play a critical role in various biological processes. Germline FOXL2 mutations have been identified in blepharophimosis/ptosis/epicanthus inversus syndrome. The somatic missense mutation in FOXL2 (FOXL2 C134W) is now known to be the defining molecular feature of adult-type granulosa cell tumour of the ovary, present in over 90% of cases of this tumour type. Immunohistochemistry for FOXL2 is used as a marker of sex cord-stromal differentiation. However, expression is not restricted to lesions harbouring FOXL2 mutations, and it is positive in a variety of sex cord-stromal proliferations other than adult-type granulosa cell tumour.
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Affiliation(s)
- Aysha Mubeen
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Carlos Parra-Herran
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts, USA
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Huang Y, Zhang L, Liu T, Liang E. LMNB1 targets FOXD1 to promote progression of prostate cancer. Exp Ther Med 2023; 26:513. [PMID: 37840569 PMCID: PMC10570766 DOI: 10.3892/etm.2023.12212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 06/09/2023] [Indexed: 10/17/2023] Open
Abstract
Forkhead box D1 (FOXD1) expression is upregulated in various types of human cancer. To the best of our knowledge, the roles of FOXD1 in prostate cancer (PC) remain largely unknown. The Cancer Genome Atlas dataset was used for the bioinformatics analysis of FOXD1 in PC. FOXD1 expression levels in normal immortalized human prostate epithelial cells (RWPE-1) and prostate cancer cells were detected by reverse transcription-quantitative PCR. PC cell viability was detected using Cell Counting Kit-8 assay. Transwell assays were performed to assess the migration and invasion of PC cells. Luciferase reporter gene assay was used to validate the association between FOXD1 and lamin (LMN)B1. LMNB1 is an important part of the cytoskeleton, which serves an important role in the process of tumor occurrence and development, regulating apoptosis and DNA repair. FOXD1 expression was upregulated in PC tissues, with its high expression being associated with clinical stage and survival in PC. Knockdown of FOXD1 inhibited viability, migration and invasion of PC cells. FOXD1 positively regulated LMNB1 expression. The effect of FOXD1 knockdown on PC cells was reversed by LMNB1 overexpression. In conclusion, FOXD1, positively regulated by LMNB1, served as an oncogene in PC and may be a potential biomarker and treatment target for PC.
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Affiliation(s)
- Yuanshe Huang
- Agriculture College, Innovation Center for Efficient Agricultural of Guizhou Mountain Characteristics, Anshun University, Anshun, Guizhou 561000, P.R. China
| | - Lai Zhang
- Agriculture College, Innovation Center for Efficient Agricultural of Guizhou Mountain Characteristics, Anshun University, Anshun, Guizhou 561000, P.R. China
| | - Tianlei Liu
- Agriculture College, Innovation Center for Efficient Agricultural of Guizhou Mountain Characteristics, Anshun University, Anshun, Guizhou 561000, P.R. China
| | - E Liang
- Agriculture College, Innovation Center for Efficient Agricultural of Guizhou Mountain Characteristics, Anshun University, Anshun, Guizhou 561000, P.R. China
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Song J, Li L, Fang Y, Lin Y, Wu L, Wan W, Wei G, Hua F, Ying J. FOXN Transcription Factors: Regulation and Significant Role in Cancer. Mol Cancer Ther 2023; 22:1028-1039. [PMID: 37566097 DOI: 10.1158/1535-7163.mct-23-0208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/12/2023]
Abstract
A growing number of studies have demonstrated that cancer development is closely linked to abnormal gene expression, including alterations in the transcriptional activity of transcription factors. The Forkhead box class N (FOXN) proteins FOXN1-6 form a highly conserved class of transcription factors, which have been shown in recent years to be involved in the regulation of malignant progression in a variety of cancers. FOXNs mediate cell proliferation, cell-cycle progression, cell differentiation, metabolic homeostasis, embryonic development, DNA damage repair, tumor angiogenesis, and other critical biological processes. Therefore, transcriptional dysregulation of FOXNs can directly affect cellular physiology and promote cancer development. Numerous studies have demonstrated that the transcriptional activity of FOXNs is regulated by protein-protein interactions, microRNAs (miRNA), and posttranslational modifications (PTM). However, the mechanisms underlying the molecular regulation of FOXNs in cancer development are unclear. Here, we reviewed the molecular regulatory mechanisms of FOXNs expression and activity, their role in the malignant progression of tumors, and their value for clinical applications in cancer therapy. This review may help design experimental studies involving FOXN transcription factors, and enhance their therapeutic potential as antitumor targets.
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Affiliation(s)
- Jiali Song
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Longshan Li
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Yang Fang
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Yue Lin
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Luojia Wu
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Wei Wan
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Gen Wei
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Fuzhou Hua
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
| | - Jun Ying
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, P.R. China
- Key Laboratory of Anesthesiology of Jiangxi Province, Nanchang City, Jiangxi Province, P.R. China
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Chuang KT, Chiou SS, Hsu SH. Recent Advances in Transcription Factors Biomarkers and Targeted Therapies Focusing on Epithelial-Mesenchymal Transition. Cancers (Basel) 2023; 15:3338. [PMID: 37444447 DOI: 10.3390/cancers15133338] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/07/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Transcription factors involve many proteins in the process of transactivating or transcribing (none-) encoded DNA to initiate and regulate downstream signals, such as RNA polymerase. Their unique characteristic is that they possess specific domains that bind to specific DNA element sequences called enhancer or promoter sequences. Epithelial-mesenchymal transition (EMT) is involved in cancer progression. Many dysregulated transcription factors-such as Myc, SNAIs, Twists, and ZEBs-are key drivers of tumor metastasis through EMT regulation. This review summarizes currently available evidence related to the oncogenic role of classified transcription factors in EMT editing and epigenetic regulation, clarifying the roles of the classified conserved transcription factor family involved in the EMT and how these factors could be used as therapeutic targets in future investigations.
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Affiliation(s)
- Kai-Ting Chuang
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- School of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shyh-Shin Chiou
- Division of Pediatric Hematology and Oncology, Department of Pediatrics, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Shih-Hsien Hsu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan
- Center of Applied Genomics, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Petrie MV, He Y, Gan Y, Ostrow AZ, Aparicio OM. Broadly Applicable Control Approaches Improve Accuracy of ChIP-Seq Data. Int J Mol Sci 2023; 24:9271. [PMID: 37298223 PMCID: PMC10252487 DOI: 10.3390/ijms24119271] [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: 04/25/2023] [Revised: 05/18/2023] [Accepted: 05/23/2023] [Indexed: 06/12/2023] Open
Abstract
Chromatin ImmunoPrecipitation (ChIP) is a widely used method for the analysis of protein-DNA interactions in vivo; however, ChIP has pitfalls, particularly false-positive signal enrichment that permeates the data. We have developed a new approach to control for non-specific enrichment in ChIP that involves the expression of a non-genome-binding protein targeted in the IP alongside the experimental target protein due to the sharing of epitope tags. ChIP of the protein provides a "sensor" for non-specific enrichment that can be used for the normalization of the experimental data, thereby correcting for non-specific signals and improving data quality as validated against known binding sites for several proteins that we tested, including Fkh1, Orc1, Mcm4, and Sir2. We also tested a DNA-binding mutant approach and showed that, when feasible, ChIP of a site-specific DNA-binding mutant of the target protein is likely an ideal control. These methods vastly improve our ChIP-seq results in S. cerevisiae and should be applicable in other systems.
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Affiliation(s)
| | | | | | | | - Oscar M. Aparicio
- Molecular and Computational Biology Section, University of Southern California, Los Angeles, CA 90089, USA; (M.V.P.); (Y.H.); (Y.G.); (A.Z.O.)
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Rani M, Kumari R, Singh SP, Devi A, Bansal P, Siddiqi A, Alsahli MA, Almatroodi SA, Rahmani AH, Rizvi MMA. MicroRNAs as master regulators of FOXO transcription factors in cancer management. Life Sci 2023; 321:121535. [PMID: 36906255 DOI: 10.1016/j.lfs.2023.121535] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/12/2023]
Abstract
MicroRNAs are critical regulators of the plethora of genes, including FOXO "forkhead" dependent transcription factors, which are bonafide tumour suppressors. The FOXO family members modulate a hub of cellular processes like apoptosis, cell cycle arrest, differentiation, ROS detoxification, and longevity. Aberrant expression of FOXOs in human cancers has been observed due to their down-regulation by diverse microRNAs, which are predominantly involved in tumour initiation, chemo-resistance and tumour progression. Chemo-resistance is a major obstacle in cancer treatment. Over 90% of casualties in cancer patients are reportedly associated with chemo-resistance. Here, we have primarily discussed the structure, functions of FOXO and also their post-translational modifications which influence the activities of these FOXO family members. Further, we have addressed the role of microRNAs in carcinogenesis by regulating the FOXOs at post-transcriptional level. Therefore, microRNAs-FOXO axis can be exploited as a novel cancer therapy. The administration of microRNA-based cancer therapy is likely to be beneficial to curb chemo-resistance in cancers.
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Affiliation(s)
- Madhu Rani
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Rashmi Kumari
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Shashi Prakash Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India; Centre for Pharmacology and Therapeutics, Rosewell Park Comprehensive Care Centre, 665 Elm Street, Buffalo, NY, USA 14203
| | - Annu Devi
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi 110067, India
| | - Preeti Bansal
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Aisha Siddiqi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Mohammed A Alsahli
- Department of Medical Laboratories, College of Applied Medical Sciences, Buraydah 51452, Saudi Arabia
| | - Saleh A Almatroodi
- Department of Medical Laboratories, College of Applied Medical Sciences, Buraydah 51452, Saudi Arabia
| | - Arshad Husain Rahmani
- Department of Medical Laboratories, College of Applied Medical Sciences, Buraydah 51452, Saudi Arabia
| | - M Moshahid Alam Rizvi
- Genome Biology Laboratory, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
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Zhou H, Shi BJ. New roles of DNA-binding and forkhead-associated domains of Fkh1 and Fkh2 in cellular functions. Cell Biochem Funct 2022; 40:888-902. [PMID: 36121195 DOI: 10.1002/cbf.3750] [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: 05/26/2022] [Revised: 09/06/2022] [Accepted: 09/07/2022] [Indexed: 12/15/2022]
Abstract
Two yeast forkhead transcription factors Fkh1 and Fkh2 regulate the transcription of CLB2 cluster genes important for mitosis. Both proteins contain a DNA-binding domain (DBD) and a forkhead-associated domain (FHAD), which are essential for ternary complex formation with transcription factor Mcm1, the transcription of CLB2 cluster genes and the physical interaction with Ndd1 and Clb2. Fkh2 also contains an additional C' domain that contains six consensus Cdk phosphorylation sites, but the function of this domain is dispensable. Here, we found new roles of the DBD, the FHAD, and the C' domain of Fkh1 and Fkh2 in cellular functions. The Fkh2 DBD determines the genetic interaction with NDD1, while both the FHAD and DBD of Fkh1 or Fkh2 determine cell morphology and stability of their own transcripts. Both HFADs, but not DBDs, also mediate physical interaction between Fkh1 and Fkh2. DBD and HFAD of Fkh1 and DBD, but not HFAD, of Fkh2 are also fundamental for nuclear localization. However, the Fkh2-specific C' domain has no role in these aspects except in the stability of some fkh mutant transcripts, which is either increased or decreased in the presence of this domain. These findings reveal that Fkh1 and Fkh2 have multiple cellular functions and function mainly via their DBD and FHAD through a domain-controlled feedback regulation mechanism.
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Affiliation(s)
- Hui Zhou
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
| | - Bu-Jun Shi
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
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Mehterov N, Sacconi A, Pulito C, Vladimirov B, Haralanov G, Pazardjikliev D, Nonchev B, Berindan-Neagoe I, Blandino G, Sarafian V. A novel panel of clinically relevant miRNAs signature accurately differentiates oral cancer from normal mucosa. Front Oncol 2022; 12:1072579. [PMID: 36531016 PMCID: PMC9753689 DOI: 10.3389/fonc.2022.1072579] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/09/2022] [Indexed: 08/27/2023] Open
Abstract
INTRODUCTION Although a considerable body of knowledge has been accumulated regarding the early diagnosis and treatment of oral squamous cell carcinoma (OSCC), its survival rates have not improved over the last decades. Thus, deciphering the molecular mechanisms governing oral cancer will support the development of even better diagnostic and therapeutic strategies. Previous studies have linked aberrantly expressed microRNAs (miRNAs) with the development of OSCC. METHODS We combined bioinformatical and molecular methods to identify miRNAs with possible clinical significance as biomarkers in OSCC. A set of 10 miRNAs were selected via an in silico approach by analysing the 3'untranslated regions (3'UTRs) of cancer-related mRNAs such as FLRT2, NTRK3, and SLC8A1, TFCP2L1 and etc. RT-qPCR was used to compare the expression of in silico identified miRNAs in OSCC and normal tissues (n=32). RESULTS Among the screened miRNAs, miR-21-5p (p < 0.0001), miR-93-5p (p < 0.0197), miR-146b-5p (p <0.0012), miR-155-5p (p < 0.0001), miR-182-5p (p < 0.0001) were significantly overexpressed, whereas miR-133b (p < 0.05) was significantly downregulated in OSCC tissues, a scenario confirmed in two additional OSCC validation cohorts: Regina Elena National Cancer Institute (IRE cohort, N=74) and The Cancer Genome Atlas Data Portal (TCGA cohort, N=354). Initial stage tumors (T1, T2) expressed significantly higher levels of miR-133b (p < 0.0004) compared to more advanced ones (T3, T4). Also, we identified miR-93-5p (p < 0.0003), miR-133b (p < 0.0017) and miR-155-5p (p < 0.0004) as correlated with HPV-induced OSCC. The high expression of these 6 miRNAs as a signature predicted shorter disease-free survival (DFS) and could efficiently distinguish OSCC cases from healthy controls with areas under the curve (AUC) of 0.91 with sensitivity and specificity of 0.98 and 0.6, respectively. Further target identification analysis revealed enrichment of genes involved in FOXO, longevity, glycan biosynthesis and p53 cancer-related signaling pathways. Also, the selected targets were underexpressed in OSCC tissues and showed clinical significance related to overall survival (OS) and DFS. DISCUSSION Our results demonstrate that a novel panel consisting of miR-21-5p, miR-93-5p, miR-133b, miR-146b-5p, miR-155-5p and miR-182-5p could be used as OSCC-specific molecular signature with diagnostic and prognostic significance related to OS and DFS.
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Affiliation(s)
- Nikolay Mehterov
- Department of Medical Biology, Medical University-Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Andrea Sacconi
- UOSD Clinical Trial Center, Biostatistics and Bioinformatics, IRCCS Regina Elena National Cancer Institute, Rome, Italy
| | - Claudio Pulito
- Translational Oncology Research Unit, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS, Regina Elena National Cancer Institute, Rome, Italy
| | - Boyan Vladimirov
- Department of Maxillofacial Surgery, Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Georgi Haralanov
- Department of Maxillofacial Surgery, Medical University-Plovdiv, Plovdiv, Bulgaria
| | | | - Boyan Nonchev
- Department of Endocrinology, Medical University-Plovdiv, Plovdiv, Bulgaria
| | - Ioana Berindan-Neagoe
- Research Center for Functional Genomics, Biomedicine and Translational Medicine, “Iuliu Hatieganu” University of Medicine and Pharmacy, Cluj-Napoca, Romania
| | - Giovanni Blandino
- Translational Oncology Research Unit, Department of Research, Advanced Diagnostic, and Technological Innovation, IRCCS, Regina Elena National Cancer Institute, Rome, Italy
| | - Victoria Sarafian
- Department of Medical Biology, Medical University-Plovdiv, Plovdiv, Bulgaria
- Research Institute, Medical University-Plovdiv, Plovdiv, Bulgaria
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Dao FY, Lv H, Fullwood MJ, Lin H. Accurate Identification of DNA Replication Origin by Fusing Epigenomics and Chromatin Interaction Information. RESEARCH (WASHINGTON, D.C.) 2022; 2022:9780293. [PMID: 36405252 PMCID: PMC9667886 DOI: 10.34133/2022/9780293] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/30/2022] [Indexed: 07/29/2023]
Abstract
DNA replication initiation is a complex process involving various genetic and epigenomic signatures. The correct identification of replication origins (ORIs) could provide important clues for the study of a variety of diseases caused by replication. Here, we design a computational approach named iORI-Epi to recognize ORIs by incorporating epigenome-based features, sequence-based features, and 3D genome-based features. The iORI-Epi displays excellent robustness and generalization ability on both training datasets and independent datasets of K562 cell line. Further experiments confirm that iORI-Epi is highly scalable in other cell lines (MCF7 and HCT116). We also analyze and clarify the regulatory role of epigenomic marks, DNA motifs, and chromatin interaction in DNA replication initiation of eukaryotic genomes. Finally, we discuss gene enrichment pathways from the perspective of ORIs in different replication timing states and heuristically dissect the effect of promoters on replication initiation. Our computational methodology is worth extending to ORI identification in other eukaryotic species.
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Affiliation(s)
- Fu-Ying Dao
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore
| | - Hao Lv
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
- Department of Molecular Life Sciences, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Melissa J. Fullwood
- School of Biological Sciences, Nanyang Technological University, Singapore 639798, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore 138673, Singapore
| | - Hao Lin
- Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China
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Elevated FOXA1 Expression Indicates Poor Prognosis in Liver Cancer due to Its Effects on Cell Proliferation and Metastasis. DISEASE MARKERS 2022; 2022:3317315. [PMID: 35968505 PMCID: PMC9374549 DOI: 10.1155/2022/3317315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 07/14/2022] [Accepted: 07/15/2022] [Indexed: 12/24/2022]
Abstract
Purpose Studying the pathogenesis of liver cancer is conducive to the exploration of effective diagnostic and prognostic biomarkers. In this study, we investigated the expression of FOXA1 and its oncogenic role in hepatocellular carcinoma (HCC). Methods Transcriptome data of HCC tissues were downloaded from The Cancer Genome Atlas (TCGA) and GEO databases and analyzed using R software. We also upregulated FOXA1 expression in HCC cells and investigated the role of FOXA1 in the proliferation and migration of HCC cells through proliferation, colony formation, wound healing, and Transwell assays. Results An analysis of the transcriptome data in TCGA database revealed found that FOXA1 is highly expressed in HCC tissues and that patients with low FOXA1 expression have a better prognosis. High FOXA1 expression was mainly associated with extracellular matrix organization, cancer, and mitosis. The results of an immunohistochemistry (IHC) assay showed that FOXA1 protein was highly expressed in HCC tissues, and patients with low FOXA1 expression showed longer disease-specific survival times and progression-free intervals. The results from quantitative reverse transcription–PCR (RT–qPCR) and Western blot experiments showed that the expression of FOXA1 in liver cancer cell lines was higher than that in immortalized human liver cell lines. Proliferation, wound healing, and Transwell experiments showed that FOXA1 enhanced the proliferation and migration abilities of liver cancer and immortalized human cell lines. Conclusion Our research suggests that FOXA1 plays an important role in promoting the recurrence and metastasis of HCC by increasing cell proliferation and metastasis.
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14
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The Expression and Survival Significance of FOXD1 in Lung Squamous Cell Carcinoma: A Meta-Analysis, Immunohistochemistry Validation, and Bioinformatics Analysis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:7798654. [PMID: 35607308 PMCID: PMC9124105 DOI: 10.1155/2022/7798654] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 04/21/2022] [Indexed: 12/24/2022]
Abstract
Accumulating evidence demonstrated that FOXD1 dysregulation was correlated with a broad spectrum of malignancies. However, litter is known about the role of FOXD1 in the progression of lung squamous cell carcinoma (LUSC). We conducted the comprehensive bioinformatics analysis to investigate FOXD1 expression in LUSC from TCGA and GEO datasets, and validated the FOXD1 expression pattern in clinical samples using immunohistochemistry method. ESTIMATE and CIBERSORT algorithms were performed to assess the relationship of FOXD1 and tumor microenvironment and immune cell infiltration. Our study showed that FOXD1 expression was significantly upregulated in LUSC tissues in TCGA dataset, validated by GEO datasets and clinical samples. In TCGA dataset, Kaplan-Meier curves showed that high FOXD1 expression was significantly correlated with favorable prognosis in LUSC patients. Moreover, FOXD1 expression has an impact on immune score and the proportions of immune cell infiltration subgroups. Finally, we predicted FOXD1 may be involved in many immune-related biological functions and cancer-related signaling pathways. Taken together, FOXD1 was upregulated in LUSC tissues, and FOXD1 expression could be a potential prognostic marker. FOXD1 might be associated with tumor microenvironment and perhaps a potential target in the tumor immunotherapy.
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Liu Y, Tu M, Wang L. Pan-Cancer Analysis Predicts FOXS1 as a Key Target in Prognosis and Tumor Immunotherapy. Int J Gen Med 2022; 15:2171-2185. [PMID: 35241932 PMCID: PMC8887970 DOI: 10.2147/ijgm.s354195] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/18/2022] [Indexed: 12/14/2022] Open
Abstract
Purpose Only a few studies have reported the role of FOXS1, a transcriptional factor, in the tumor development process. In this article, we investigate the function of FOXS1 in distinct neoplastic development and the tumor immune microenvironment (TIME). Patients and Methods The latent roles of FOXS1 in various tumors were prospected based on TCGA, GTEx, CCLE, GEPIA2, cBioPortal, TIMER, ImmuCellAI databases, GSVA datasets, GSEA datasets, and R packages. The expression difference, gene alteration, clinical characteristics, prognostic values, biological mechanism, potential pathways, tumor microenvironment, and immune cell infiltration related to FOXS1 were appraised. Results FOXS1 was strongly expressed in pan-cancer, and this gene was associated with low survival rates. FOXS1 was linked to many pathways that are cancer-promoting and immune-related. The expression of this transcriptional factor in cancers was positively related to immune cell infiltration, especially M2-like macrophages and Treg cells. In addition to that, FOXS1 demonstrated a positive relationship with many immune-suppression genes, such as TGFB1 and ARORA2A. Conclusion Our study identified an oncogenic effect of FOXS1, which may play a vital role as a prognosticative biological marker in pan-cancer. Exorbitant expression of FOXS1 is associated with high TAMs and Treg cells infiltration. These cells have an immunosuppressive function and promote the development of the immunosuppressive tumor microenvironment. The research of FOXS1 provided a potential drug target for tumor immunotherapy.
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Affiliation(s)
- Yunqiang Liu
- School of Medical College, Guangdong Medical University, Zhanjiang, Guang Dong Province, 524023, People’s Republic of China
| | - Mengjun Tu
- Eye Hospital and School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang Province, 325027, People’s Republic of China
- National Clinical Research Center for Ocular Diseases, Wenzhou, Zhejiang Province, 325027, People’s Republic of China
| | - Lingling Wang
- Department of Clinical Laboratory Center of the Second Affiliated Hospital & Yu Ying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, 325027, People’s Republic of China
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, 325035, People’s Republic of China
- Correspondence: Lingling Wang, Department of Clinical Laboratory Center of The Second Affiliated Hospital & Yu Ying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, 325027, People’s Republic of China, Tel +8618867786629, Email
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16
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Li J, Yan T, Wu X, Ke X, Li X, Zhu Y, Yang J, Li Z. Aberrant overexpression of transcription factor Forkhead box D1 predicts poor prognosis and promotes cancer progression in HNSCC. BMC Cancer 2021; 21:1205. [PMID: 34772357 PMCID: PMC8588630 DOI: 10.1186/s12885-021-08868-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 08/28/2021] [Indexed: 01/01/2023] Open
Abstract
Objectives Forkhead box D1, the core transcription factor member of FOX family, has gradually seen as a key cancerous regulatory. However, its expression and carcinogenicity in head and neck squamous cell carcinoma (HNSCC) have not been reported yet. This study was to investigate its expression pattern, clinicopathological significance and biological roles in HNSCC. Methods HNSCC data from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) was used to indicate the detailed expression pattern and outcome association of FOXD1, while Western Blot assay to detect FOXD1 level in a panel of HNSCC cell lines as well as immunocytochemistry to explore FOXD1 protein abundance and sublocation. Series of siRNA-mediated FOXD1 knock-down experiments to assess the proliferation, migration, invasion and anti- apoptosis ability after FOXD1 down-regulation. Bioinformatic analysis to find out which biological function and cancer-related pathways of FOXD1 associated genes involved in. Results FOXD1 mRNA was significantly overexpressed in TCGA-HNSCC, GSE6631, GSE12452, GSE25099 and GSE30784. Besides, IHC results shown that nuclear location FOXD1 protein was significantly higher in primary HNSCC specimens from cohort involved in this study. Also, FOXD1 abundance was significantly correlated with cervical node metastasis and poor over-all/disease-free survival after combination analysis with patient pathological information. siRNA-mediated FOXD1 knock-down significantly inhibited cell proliferation, migration and invasion and induced apoptosis in HNSCC cells. Further analysis of GSEA, GO and KEGG showed that FOXD1 expression was significantly associated with oncological function and cancer-related pathways. Conclusions Taken together, our study implies that the potential oncogene, FOXD1, facilitates oncological behavior who can be identified as a brand-new HNSCC biomarker with diagnostic and prognostic significance. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08868-4.
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Affiliation(s)
- Jin Li
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210029, Jiangsu, China.,Jiangsu Province Engineering Research Canter of Stomatological Translation Medicine, Nanjing, Jiangsu, China
| | - Tingyuan Yan
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, Jiangsu, People's Republic of China.,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210029, Jiangsu, China.,Jiangsu Province Engineering Research Canter of Stomatological Translation Medicine, Nanjing, Jiangsu, China
| | - Xiang Wu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Xueping Ke
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Xin Li
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Yumin Zhu
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Jianrong Yang
- Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210029, Jiangsu, China
| | - Zhongwu Li
- Department of Oral and Maxillofacial Surgery, The Affiliated Stomatological Hospital of Nanjing Medical University, 136 Hanzhong Road, Nanjing, 210029, Jiangsu, People's Republic of China. .,Jiangsu Key Laboratory of Oral Diseases, Nanjing Medical University, Nanjing, 210029, Jiangsu, China. .,Jiangsu Province Engineering Research Canter of Stomatological Translation Medicine, Nanjing, Jiangsu, China.
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17
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Chen YH, Li CL, Chen WJ, Liu J, Wu HT. Diverse roles of FOXO family members in gastric cancer. World J Gastrointest Oncol 2021; 13:1367-1382. [PMID: 34721771 PMCID: PMC8529928 DOI: 10.4251/wjgo.v13.i10.1367] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 07/06/2021] [Accepted: 08/13/2021] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is the fifth most diagnosed cancer and the third leading cause of cancer-related death worldwide. Although progress has been made in diagnosis, surgical resection, systemic chemotherapy, and immunotherapy, patients with GC still have a poor prognosis. The overall 5-year survival rate in patients with advanced GC is less than 5%. The FOXO subfamily, of the forkhead box family of transcription factors, consists of four members, FOXO1, FOXO3, FOXO4, and FOXO6. This subfamily plays an important role in many cellular processes, such as cell cycle, cell growth, apoptosis, autophagy, stress resistance, protection from aggregate toxicity, DNA repair, tumor suppression, and metabolism, in both normal tissue and malignant tumors. Various studies support a role for FOXOs as tumor suppressors based on their ability to inhibit angiogenesis and metastasis, and promote apoptosis, yet several other studies have shown that FOXOs might also promote tumor progression in certain circumstances. To elucidate the diverse roles of FOXOs in GC, this article systematically reviews the cellular functions of FOXOs in GC to determine potential therapeutic targets and treatment strategies for patients with GC.
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Affiliation(s)
- Yu-Han Chen
- Department of Clinical Medicine, Shantou University Medical College, Shantou 515041, Guangdong Province, China
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Changjiang Scholar's Laboratory, Department of Physiology, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Chun-Lan Li
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Changjiang Scholar's Laboratory, Department of Physiology, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Wen-Jia Chen
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Changjiang Scholar's Laboratory, Department of Physiology, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Jing Liu
- Guangdong Provincial Key Laboratory for Diagnosis and Treatment of Breast Cancer, Changjiang Scholar's Laboratory, Department of Physiology, Shantou University Medical College, Shantou 515041, Guangdong Province, China
| | - Hua-Tao Wu
- Department of General Surgery, The First Affiliated Hospital of Shantou University Medical College, Shantou 515041, Guangdong Province, China
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18
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Nair KS, Srivastava C, Brown RV, Koli S, Choquet H, Kang HS, Kuo YM, Grimm SA, Sutherland C, Badea A, Johnson GA, Zhao Y, Yin J, Okamoto K, Clark G, Borrás T, Zode G, Kizhatil K, Chakrabarti S, John SWM, Jorgenson E, Jetten AM. GLIS1 regulates trabecular meshwork function and intraocular pressure and is associated with glaucoma in humans. Nat Commun 2021; 12:4877. [PMID: 34385434 PMCID: PMC8361148 DOI: 10.1038/s41467-021-25181-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 07/21/2021] [Indexed: 01/01/2023] Open
Abstract
Chronically elevated intraocular pressure (IOP) is the major risk factor of primary open-angle glaucoma, a leading cause of blindness. Dysfunction of the trabecular meshwork (TM), which controls the outflow of aqueous humor (AqH) from the anterior chamber, is the major cause of elevated IOP. Here, we demonstrate that mice deficient in the Krüppel-like zinc finger transcriptional factor GLI-similar-1 (GLIS1) develop chronically elevated IOP. Magnetic resonance imaging and histopathological analysis reveal that deficiency in GLIS1 expression induces progressive degeneration of the TM, leading to inefficient AqH drainage from the anterior chamber and elevated IOP. Transcriptome and cistrome analyses identified several glaucoma- and extracellular matrix-associated genes as direct transcriptional targets of GLIS1. We also identified a significant association between GLIS1 variant rs941125 and glaucoma in humans (P = 4.73 × 10-6), further supporting a role for GLIS1 into glaucoma etiology. Our study identifies GLIS1 as a critical regulator of TM function and maintenance, AqH dynamics, and IOP.
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Affiliation(s)
- K Saidas Nair
- Department of Ophthalmology and Department of Anatomy, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Chitrangda Srivastava
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Robert V Brown
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Swanand Koli
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Hélène Choquet
- Kaiser Permanente Northern California, Division of Research, Oakland, CA, USA
| | - Hong Soon Kang
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Yien-Ming Kuo
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sara A Grimm
- Integrative Bioinformatics Support Group, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Caleb Sutherland
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | - Alexandra Badea
- Center for In Vivo Microscopy, Department of Radiology, Duke University, Durham, NC, USA
| | - G Allan Johnson
- Center for In Vivo Microscopy, Department of Radiology, Duke University, Durham, NC, USA
| | - Yin Zhao
- Department of Ophthalmology, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Jie Yin
- Kaiser Permanente Northern California, Division of Research, Oakland, CA, USA
| | - Kyoko Okamoto
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA
| | | | - Terete Borrás
- Department of Ophthalmology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Gulab Zode
- Department of Pharmacology and Neuroscience, North Texas Eye Research Institute, University of North Texas Health Science Center, Fort Worth, TX, USA
| | | | | | - Simon W M John
- The Jackson Laboratory, Bar Harbor, ME, USA
- Howard Hughes Medical Institute, Mortimer B. Zuckerman Mind Brain Behavior Institute, Department of Ophthalmology, Columbia University, New York, NY, USA
| | | | - Anton M Jetten
- Immunity, Inflammation and Disease Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
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19
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Xi H, He Z, Lv C. FOXG1 improves mitochondrial function and promotes the progression of nasopharyngeal carcinoma. Mol Med Rep 2021; 24:651. [PMID: 34278485 PMCID: PMC8299199 DOI: 10.3892/mmr.2021.12290] [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: 10/10/2020] [Accepted: 05/14/2021] [Indexed: 12/28/2022] Open
Abstract
Forkhead‑box gene 1 (FOXG1) has been reported to serve an important role in various malignancies, but its effects on nasopharyngeal cancer (NPC) remain unknown. Thus, the present study aimed to investigate the specific regulatory relationship between FOXG1 and NPC progression. Tumor tissues and matching para‑carcinoma tissues were obtained from patients with NPC. Small interfering (si)RNA‑FOXG1 and pcDNA3.1‑FOXG1 were transfected into SUNE‑1 and C666‑1 cells to knockdown and overexpress FOXG1 expression, respectively. FOXG1 expression was detected using reverse transcription‑quantitative PCR and immunohistochemistry. Cell proliferation was detected using MTT and 5‑ethynyl‑20‑deoxyuridine assays. Transwell invasion assay, wound healing assay and flow cytometry were used to detect cell invasion, migration and apoptosis, respectively. Western blotting was conducted to detect the expression levels of mitochondrial markers (succinate dehydrogenase complex flavoprotein subunit A, heat shock protein 60 and pyruvate dehydrogenase), epithelial‑mesenchymal transition (EMT) related proteins (N‑cadherin, Snail and E‑cadherin) and apoptosis‑related proteins [Bax, Bcl‑2, poly(ADP‑ribose) polymerase 1 (PARP), cleaved PARP, cleaved caspase‑3, cleaved caspase‑8, cleaved caspase‑9, caspase‑3, caspase‑8 and caspase‑9]. The mitochondrial membrane potential was detected via flow cytometry, while the ATP/ADP ratio was determined using the ADP/ATP ratio assay kit. The present results demonstrated that FOXG1 expression was upregulated in NPC tissues and cells, and was associated with distant metastasis and TNM stage. Moreover, knockdown of FOXG1 inhibited the proliferation, migration, invasion, EMT and mitochondrial function of SUNE‑1 cells, as well as promoted cell apoptosis, while the opposite results were observed in C666‑1 cells. In conclusion, FOXG1 enhanced proliferation, migration and invasion, induced EMT and improved mitochondrial function in NPC cells. The current findings provide an adequate theoretical basis for the treatment of NPC.
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Affiliation(s)
- Huajun Xi
- Department of Otolaryngology and Stomatology, Shouguang People's Hospital, Shouguang, Shandong 262700, P.R. China
| | - Zhengxiang He
- Department of Otolaryngology and Maxillofacial Surgery, Wuwei People's Hospital, Wuwei, Gansu 733000, P.R. China
| | - Cao Lv
- Department of Otolaryngology, Head and Neck Surgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650101, P.R. China
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20
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Quantitative model of eukaryotic Cdk control through the Forkhead CONTROLLER. NPJ Syst Biol Appl 2021; 7:28. [PMID: 34117265 PMCID: PMC8196193 DOI: 10.1038/s41540-021-00187-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 05/07/2021] [Indexed: 12/20/2022] Open
Abstract
In budding yeast, synchronization of waves of mitotic cyclins that activate the Cdk1 kinase occur through Forkhead transcription factors. These molecules act as controllers of their sequential order and may account for the separation in time of incompatible processes. Here, a Forkhead-mediated design principle underlying the quantitative model of Cdk control is proposed for budding yeast. This design rationalizes timing of cell division, through progressive and coordinated cyclin/Cdk-mediated phosphorylation of Forkhead, and autonomous cyclin/Cdk oscillations. A “clock unit” incorporating this design that regulates timing of cell division is proposed for both yeast and mammals, and has a DRIVER operating the incompatible processes that is instructed by multiple CLOCKS. TIMERS determine whether the clocks are active, whereas CONTROLLERS determine how quickly the clocks shall function depending on external MODULATORS. This “clock unit” may coordinate temporal waves of cyclin/Cdk concentration/activity in the eukaryotic cell cycle making the driver operate the incompatible processes, at separate times.
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21
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Zhou LB, Cao Q, Ding Q, Sun WL, Li ZY, Zhao M, Lin XW, Zhou GP, Fan WX. Transcription factor FOXC1 positively regulates SFRP1 expression in androgenetic alopecia. Exp Cell Res 2021; 404:112618. [PMID: 33965401 DOI: 10.1016/j.yexcr.2021.112618] [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: 11/30/2020] [Revised: 04/13/2021] [Accepted: 04/17/2021] [Indexed: 11/19/2022]
Abstract
Androgenetic alopecia (AGA) is the most common type of hair loss dysfunction. Secreted frizzled related protein 1 (SFRP1) is found to be associated with hair loss, but its role in AGA and the regulation mechanism of its transcription level is unclear. The aim of our study is to explore the expression of SFRP1 in AGA samples and its transcriptional mechanism. Male frontal and occipital scalp hair follicles from AGA patients were collected, and human dermal papilla cells (DPCs) were isolated and cultured. SFRP1 gene was cloned and constructed into recombinant plasmids to perform dual-luciferase reporter assay. Transcription factor binding sites were predicted through the Jaspar website and further confirmed by the chromatin immunoprecipitation (ChIP) assay. Expression of genes in DPCs was determined by immunofluorescence (IF) staining, quantitative real-time PCR (qRT-PCR) and western blotting. Our findings showed that SFRP1 was highly expressed in DPCs of AGA patients. The core promoter region of SFRP1 was from -100 to +50 bp and was found to be positively regulated by forkhead box C1 (FOXC1), a transcription factor related to hair growth, both at mRNA and protein level in DPCs. Our study suggests that FOXC1 plays an important role in regulating SFRP1 transcription, which may provide new insights into the development of therapeutic strategies for the treatment of AGA.
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Affiliation(s)
- Lan-Bo Zhou
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Qian Cao
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Qi Ding
- Department of Dermatology, Affiliated Hospital of Nantong University, Nantong, Jiangsu Province, China
| | - Wei-Ling Sun
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Zhi-Yu Li
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Min Zhao
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Xue-Wen Lin
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Guo-Ping Zhou
- Department of Pediatrics, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Wei-Xin Fan
- Department of Dermatology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.
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22
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Luo Y, Liu F, Ma J, Fu Y, Gui R. A novel epigenetic regulation of circFoxp1 on Foxp1 in colon cancer cells. Cell Death Dis 2020; 11:782. [PMID: 32951006 PMCID: PMC7502072 DOI: 10.1038/s41419-020-03007-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/07/2020] [Accepted: 09/09/2020] [Indexed: 01/17/2023]
Abstract
Foxp1 is a tumor suppressor in colon cancer. However, circFoxp1 derived from Foxp1 is an oncogene. In this study, we aim to investigate the role of circFoxp1 in colon cancer and the regulatory mechanism between circFoxp1 and Foxp1. 78 human colon tumor tissues and the matched paracancerous tissues were collected. Quantitative polymerase chain reaction, immunohistochemistry, quantitative methylation-specific PCR, chromatin immunoprecipitation assay, CCK-8 assay, and Tumor xenograft in nude mice were performed. The expression of circFoxp1 was increased and Foxp1 was reduced in colon cancer tissues, which were associated with a poor overall survival rate of the patients with colon cancer. CircFoxp1 recruited DNMT1 to the promoter of Foxp1, leading to promotor hypermethylation, thereby inhibiting Foxp1 transcription. Interfering circFoxp1 by siRNA in SW620 cells significantly inhibited cell viability, while knockdown Foxp1 expression partially restored SW620 cell viability. In addition, knockdown of circFoxp1 significantly sensitized colon cancer cells to Capecitabine in vitro and vivo through regulating Foxp1. We discovered a novel epigenetic pathway that circFoxp1 regulated Foxp1 in colon cancer cells. CircFoxp1 may regulate DNA methylation and demethylation to coordinate colon cancer cell proliferation and participate in chemotherapy drug responses. Therefore, circFoxp1 may be a potential therapeutic target for colon cancer.
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Affiliation(s)
- Yanwei Luo
- Department of Blood Transfusion, the Third Xiangya Hospital of Central South University, 410013, Changsha, Hunan, China
| | - Fengxia Liu
- Department of Blood Transfusion, the Third Xiangya Hospital of Central South University, 410013, Changsha, Hunan, China
| | - Jinqi Ma
- Department of Blood Transfusion, the Third Xiangya Hospital of Central South University, 410013, Changsha, Hunan, China
| | - Yunfeng Fu
- Department of Blood Transfusion, the Third Xiangya Hospital of Central South University, 410013, Changsha, Hunan, China.
| | - Rong Gui
- Department of Blood Transfusion, the Third Xiangya Hospital of Central South University, 410013, Changsha, Hunan, China.
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Shi D, Zhang K, Li G, Zhao Y. MiR-1471 protects the aggravation of non-small-cell lung carcinoma by targeting FOXL1. Biofactors 2020; 46:734-742. [PMID: 33045131 DOI: 10.1002/biof.1661] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/26/2020] [Accepted: 05/29/2020] [Indexed: 12/16/2022]
Abstract
This study detected the expression pattern of miR-1471 in non-small-cell lung cancer (NSCLC) tissues, and analyzed the prognostic significance of miR-1471 in NSCLC. Subsequently, potential targets of miR-1471 were screened for assessing the potential molecular mechanism in NSCLC. A total of 47 primary NSCLC cases treated by radical resection and systematic lymphadenectomy in the department of thoracic surgery were collected, as well as their clinical data. MiR-1471 levels in NSCLC tissues were detected by quantitative real-time polymerase chain reaction. The prognostic potential of miR-1471 in NSCLC was assessed by Kaplan-Meier method, followed by log-rank test. Potential target genes of miR-1471 and the binding sites were predicted by bioinformatics analysis, and screened for the optimal one. The binding relationship between miR-1471 and the target FOXL1 was examined by dual-luciferase reporter assay. Subsequently, biological functions of miR-1471 and FOXL1 in NSCLC cell functions were explored by cell counting kit-8 (CCK-8), 5-ethynyl-2'-deoxyuridine (EdU) assay and flow cytometry. MiR-1471 was downregulated in NSCLC tissues and its level was correlated to TNM staging in NSCLC patients. Overall survival was poor in NSCLC patients expressing low level of miR-1471. Overexpression of miR-1471 attenuated proliferative ability and arrested cell cycle progression in G1/S phase. FOXL1 was confirmed to be the target gene binding miR-1471. Its expression pattern and biological functions in NSCLC cells were contrary to those of miR-1471. MiR-1471 is downregulated in NSCLC samples, which is related to TNM staging and prognosis in NSCLC patients. Therefore, miR-1471 suppresses the malignant aggravation of NSCLC via inhibiting the translation of FOXL1 mRNA. In addition, it could be used as an effective biomarker for predicting the prognosis in NSCLC.
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Affiliation(s)
- Donglei Shi
- Department of Thoracic Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Kun Zhang
- Department of Research Center, The Second Hospital of Jilin University, Changchun, China
| | - Guangquan Li
- Department of Research Center, The Second Hospital of Jilin University, Changchun, China
| | - Yinghao Zhao
- Department of Thoracic Surgery, The Second Hospital of Jilin University, Changchun, China
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