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Steiner D, Sultan L, Sullivan T, Liu H, Zhang S, LeClerc A, Alekseyev YO, Liu G, Mazzilli SA, Zhang J, Rieger-Christ K, Burks EJ, Beane J, Lenburg ME. Identification of a gene expression signature of vascular invasion and recurrence in stage I lung adenocarcinoma via bulk and spatial transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597993. [PMID: 38915565 PMCID: PMC11195124 DOI: 10.1101/2024.06.07.597993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Microscopic vascular invasion (VI) is predictive of recurrence and benefit from lobectomy in stage I lung adenocarcinoma (LUAD) but is difficult to assess in resection specimens and cannot be accurately predicted prior to surgery. Thus, new biomarkers are needed to identify this aggressive subset of stage I LUAD tumors. To assess molecular and microenvironment features associated with angioinvasive LUAD we profiled 162 resected stage I tumors with and without VI by RNA-seq and explored spatial patterns of gene expression in a subset of 15 samples by high-resolution spatial transcriptomics (stRNA-seq). Despite the small size of invaded blood vessels, we identified a gene expression signature of VI from the bulk RNA-seq discovery cohort (n=103) and found that it was associated with VI foci, desmoplastic stroma, and high-grade patterns in our stRNA-seq data. We observed a stronger association with high-grade patterns from VI+ compared with VI- tumors. Using the discovery cohort, we developed a transcriptomic predictor of VI, that in an independent validation cohort (n=60) was associated with VI (AUROC=0.86; p=5.42×10-6) and predictive of recurrence-free survival (HR=1.98; p=0.024), even in VI- LUAD (HR=2.76; p=0.003). To determine our VI predictor's robustness to intra-tumor heterogeneity we used RNA-seq data from multi-region sampling of stage I LUAD cases in TRACERx, where the predictor scores showed high correlation (R=0.87, p<2.2×10-16) between two randomly sampled regions of the same tumor. Our study suggests that VI-associated gene expression changes are detectable beyond the site of intravasation and can be used to predict the presence of VI. This may enable the prediction of angioinvasive LUAD from biopsy specimens, allowing for more tailored medical and surgical management of stage I LUAD.
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Affiliation(s)
- Dylan Steiner
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Lila Sultan
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Travis Sullivan
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, MA, USA
| | - Hanqiao Liu
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Sherry Zhang
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Ashley LeClerc
- Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA
| | - Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Gang Liu
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Sarah A Mazzilli
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Jiarui Zhang
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Kimberly Rieger-Christ
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, MA, USA
| | - Eric J Burks
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Jennifer Beane
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Marc E Lenburg
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA, Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
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Wu Q, Berglund AE, Macaulay RJ, Etame AB. The Role of Mesenchymal Reprogramming in Malignant Clonal Evolution and Intra-Tumoral Heterogeneity in Glioblastoma. Cells 2024; 13:942. [PMID: 38891074 PMCID: PMC11171993 DOI: 10.3390/cells13110942] [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: 04/30/2024] [Revised: 05/26/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
Glioblastoma (GBM) is the most common yet uniformly fatal adult brain cancer. Intra-tumoral molecular and cellular heterogeneities are major contributory factors to therapeutic refractoriness and futility in GBM. Molecular heterogeneity is represented through molecular subtype clusters whereby the proneural (PN) subtype is associated with significantly increased long-term survival compared to the highly resistant mesenchymal (MES) subtype. Furthermore, it is universally recognized that a small subset of GBM cells known as GBM stem cells (GSCs) serve as reservoirs for tumor recurrence and progression. The clonal evolution of GSC molecular subtypes in response to therapy drives intra-tumoral heterogeneity and remains a critical determinant of GBM outcomes. In particular, the intra-tumoral MES reprogramming of GSCs using current GBM therapies has emerged as a leading hypothesis for therapeutic refractoriness. Preventing the intra-tumoral divergent evolution of GBM toward the MES subtype via new treatments would dramatically improve long-term survival for GBM patients and have a significant impact on GBM outcomes. In this review, we examine the challenges of the role of MES reprogramming in the malignant clonal evolution of glioblastoma and provide future perspectives for addressing the unmet therapeutic need to overcome resistance in GBM.
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Affiliation(s)
- Qiong Wu
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Anders E. Berglund
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Robert J. Macaulay
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
| | - Arnold B. Etame
- Department of Neuro-Oncology, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, FL 33612, USA
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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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Zhang M, Wu K, Zhang W, Lin X, Cao Q, Zhang L, Chen K. The therapeutic potential of targeting the CHD protein family in cancer. Pharmacol Ther 2024; 256:108610. [PMID: 38367868 PMCID: PMC10942663 DOI: 10.1016/j.pharmthera.2024.108610] [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: 09/28/2023] [Revised: 01/06/2024] [Accepted: 02/02/2024] [Indexed: 02/19/2024]
Abstract
Accumulating evidence indicates that epigenetic events undergo deregulation in various cancer types, playing crucial roles in tumor development. Among the epigenetic factors involved in the epigenetic remodeling of chromatin, the chromodomain helicase DNA-binding protein (CHD) family frequently exhibits gain- or loss-of-function mutations in distinct cancer types. Therefore, targeting CHD remodelers holds the potential for antitumor treatment. In this review, we discuss epigenetic regulations of cancer development. We emphasize proteins in the CHD family, delving deeply into the intricate mechanisms governing their functions. Additionally, we provide an overview of current therapeutic strategies targeting CHD family members in preclinical trials. We further discuss the promising approaches that have demonstrated early signs of success in cancer treatment.
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Affiliation(s)
- Min Zhang
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Kaiyuan Wu
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Weijie Zhang
- Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China; Department of Orthopaedic Surgery, Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xia Lin
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Qi Cao
- Department of Urology, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
| | - Kaifu Chen
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA; Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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Otani R, Sadato D, Yamada R, Yajima H, Kawamura S, Shimizu S, Tanaka S, Takayanagi S, Takami H, Yamaguchi T. CHD5 gene variant predicts leptomeningeal metastasis after surgical resection of brain metastases of breast cancer. J Neurooncol 2023; 163:657-662. [PMID: 37440096 DOI: 10.1007/s11060-023-04381-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/22/2023] [Indexed: 07/14/2023]
Abstract
PURPOSE Leptomeningeal metastasis (LM) is a complication of surgery for brain metastasis and is a risk factor of poor prognosis. The risk of LM is particularly high after surgery for a breast cancer metastasis to the brain. If the risk of LM after surgical resection for a brain metastasis were predictable, appropriate adjuvant therapy could be administered to individual patients to improve their prognosis. The present study aimed to reveal the genetic characteristics of brain metastases as means of predicting LM in breast cancer patients. METHODS Ten patients with brain metastases of breast cancer presented LM after surgical resection were analyzed by whole-exome sequencing. RESULTS A chromodomain-helicase-DNA-binding protein 5 (CHD5) gene alteration was detected in nine cases (90%), including a nonsynonymous variant in four cases and copy number deletion in five cases. CHD5 protein expression was lost in nine cases and had decreased in one case. The frequency of CHD5 gene alteration in brain metastases with LM was significantly higher than in primary breast cancer (2.3%) or in brain metastases of breast cancer (0%) (p < 0.0001). CONCLUSIONS These results suggested that the CHD5 gene alteration was associated with LM after surgical resection of breast cancer brain metastases. Searching for the gene alteration might predict the LM risk after surgical resection.
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Affiliation(s)
- Ryohei Otani
- Department of Neurosurgery, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, 3-18-22 Honkomagome, Bunkyo-ku, Tokyo, 113-8677, Japan.
| | - Daichi Sadato
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, 3-18-22 Honkomagome, Bunkyo-ku, Tokyo, 113-8677, Japan
| | - Ryoji Yamada
- Department of Neurosurgery, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, 3-18-22 Honkomagome, Bunkyo-ku, Tokyo, 113-8677, Japan
| | - Hirohisa Yajima
- Department of Neurosurgery, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, 3-18-22 Honkomagome, Bunkyo-ku, Tokyo, 113-8677, Japan
| | - Shinji Kawamura
- Department of Neurosurgery, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, 3-18-22 Honkomagome, Bunkyo-ku, Tokyo, 113-8677, Japan
| | - Sakura Shimizu
- Department of Neurosurgery, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, 3-18-22 Honkomagome, Bunkyo-ku, Tokyo, 113-8677, Japan
| | - Shota Tanaka
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Shunsaku Takayanagi
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Hirokazu Takami
- Department of Neurosurgery, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8655, Japan
| | - Tatsuro Yamaguchi
- Department of Clinical Genetics, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, 3-18-22 Honkomagome, Bunkyo-ku, Tokyo, 113-0021, Japan
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Parfenyev SE, Shabelnikov SV, Tolkunova EN, Barlev NA, Mittenberg AG. p53 Affects Zeb1 Interactome of Breast Cancer Stem Cells. Int J Mol Sci 2023; 24:9806. [PMID: 37372954 DOI: 10.3390/ijms24129806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/02/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
P53 is a critical tumor suppressor that protects the integrity of genome and prevents cells from malignant transformation, including metastases. One of the driving forces behind the onset of metastases is the epithelial to mesenchymal transition (EMT) program. Zeb1 is one of the key transcription factors that govern EMT (TF-EMT). Therefore, the interaction and mutual influence of p53 and Zeb1 plays a critical role in carcinogenesis. Another important feature of tumors is their heterogeneity mediated by the presence of so-called cancer stem cells (CSCs). To this end, we have developed a novel fluorescent reporter-based approach to enrich the population of CSCs in MCF7 cells with inducible expression of Zeb1. Using these engineered cell lines, we studied the effect of p53 on Zeb1 interactomes isolated from both CSCs and regular cancer cells. By employing co-immunoprecipitations followed by mass spectrometry, we found that the composition of Zeb1 interactome was affected not only by the p53 status but also by the level of Oct4/Sox2 expression, indicating that stemness likely affects the specificity of Zeb1 interactions. This study, together with other proteomic studies of TF-EMT interactomes, provides a framework for future molecular analyses of biological functions of Zeb1 at all stages of oncogenesis.
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Affiliation(s)
- Sergey E Parfenyev
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Sergey V Shabelnikov
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Elena N Tolkunova
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Nickolai A Barlev
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
- Department of Biomedical Sciences, School of Medicine, Nazarbayev University, Astana 20000, Kazakhstan
| | - Alexey G Mittenberg
- Institute of Cytology of the Russian Academy of Sciences, St. Petersburg 194064, Russia
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7
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Davidson RK, Kanojia S, Wu W, Kono T, Xu J, Osmulski M, Bone RN, Casey N, Evans-Molina C, Sims EK, Spaeth JM. The Chd4 Helicase Regulates Chromatin Accessibility and Gene Expression Critical for β-Cell Function In Vivo. Diabetes 2023; 72:746-757. [PMID: 36913741 PMCID: PMC10202766 DOI: 10.2337/db22-0939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 03/01/2023] [Indexed: 03/15/2023]
Abstract
The transcriptional activity of Pdx1 is modulated by a diverse array of coregulatory factors that govern chromatin accessibility, histone modifications, and nucleosome distribution. We previously identified the Chd4 subunit of the nucleosome remodeling and deacetylase complex as a Pdx1-interacting factor. To identify how loss of Chd4 impacts glucose homeostasis and gene expression programs in β-cells in vivo, we generated an inducible β-cell-specific Chd4 knockout mouse model. Removal of Chd4 from mature islet β-cells rendered mutant animals glucose intolerant, in part due to defects in insulin secretion. We observed an increased ratio of immature-to-mature insulin granules in Chd4-deficient β-cells that correlated with elevated levels of proinsulin both within isolated islets and from plasma following glucose stimulation in vivo. RNA sequencing and assay for transposase-accessible chromatin with sequencing showed that lineage-labeled Chd4-deficient β-cells have alterations in chromatin accessibility and altered expression of genes critical for β-cell function, including MafA, Slc2a2, Chga, and Chgb. Knockdown of CHD4 from a human β-cell line revealed similar defects in insulin secretion and alterations in several β-cell-enriched gene targets. These results illustrate how critical Chd4 activities are in controlling genes essential for maintaining β-cell function. ARTICLE HIGHLIGHTS Pdx1-Chd4 interactions were previously shown to be compromised in β-cells from human donors with type 2 diabetes. β-Cell-specific removal of Chd4 impairs insulin secretion and leads to glucose intolerance in mice. Expression of key β-cell functional genes and chromatin accessibility are compromised in Chd4-deficient β-cells. Chromatin remodeling activities enacted by Chd4 are essential for β-cell function under normal physiological conditions.
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Affiliation(s)
- Rebecca K. Davidson
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Sukrati Kanojia
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Wenting Wu
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN
| | - Tatsuyoshi Kono
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Jerry Xu
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Meredith Osmulski
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Robert N. Bone
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Nolan Casey
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
| | - Carmella Evans-Molina
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN
- Richard L. Roudebush Veterans’ Administration Medical Center, Indianapolis, IN
| | - Emily K. Sims
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
| | - Jason M. Spaeth
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN
- Center for Diabetes and Metabolic Diseases, Indiana University School of Medicine, Indianapolis, IN
- Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN
- Department of Anatomy, Cell Biology, and Physiology, Indiana University School of Medicine, Indianapolis, IN
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Na W, Lee IJ, Koh I, Kwon M, Song YS, Lee SH. Cancer-specific functional profiling in microsatellite-unstable (MSI) colon and endometrial cancers using combined differentially expressed genes and biclustering analysis. Medicine (Baltimore) 2023; 102:e33647. [PMID: 37171359 PMCID: PMC10174364 DOI: 10.1097/md.0000000000033647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
Microsatellite-unstable (MSI) cancers have distinct genetic and clinical features from microsatellite-stable cancers, but the molecular functional differences between MSI cancers originating from different tissues or organs have not been well studied because the application of usual differentially expressed gene (DEG) analysis is error-prone, producing too many noncancer-specific normally functioning genes. To maximize therapeutic efficacy, biomarkers reflecting cancer-specific differences between MSI cancers of different tissue origins should be identified. To identify functional differences between MSI colon and endometrial cancers, we combined DEG analysis and biclustering instead of DEG analysis alone and refined functionally relevant biclusters reflecting genuine functional differences between the 2 tumors. Specifically, using The Cancer Genome Atlas and genome-tissue expression as data sources, gene ontology (GO) enrichment tests were performed after routinely identifying DEGs between the 2 tumors with the exclusion of DEGs identified in their normal counterparts. Cancer-specific biclusters and associated enriched GO terms were obtained by biclustering with enrichment tests for the preferences for cancer type (either colon or endometrium) and GO enrichment tests for each cancer-specific bicluster, respectively. A novel childness score was developed to select functionally relevant biclusters among cancer-specific biclusters based on the extent to which the enriched GO terms of the biclusters tended to be child terms of the enriched GO terms in DEGs. The selected biclusters were tested using survival analysis to validate their clinical significance. We performed multiple sequential analyses to produce functionally relevant biclusters from the RNA sequencing data of MSI colon and endometrial cancer samples and their normal counterparts. We identified 3066 cancer-specific DEGs. Biclustering analysis revealed 153 biclusters and 41 cancer-specific biclusters were selected using Fisher exact test. A mean childness score over 0.6 was applied as the threshold and yielded 8 functionally relevant biclusters from cancer-specific biclusters. Functional differences appear to include gland cavitation and the TGF-β receptor, G protein, and cytokine pathways. In the survival analysis, 6 of the 8 functionally relevant biclusters were statistically significant. By attenuating noise and applying a synergistic contribution of DEG results, we refined candidate biomarkers to complement tissue-specific features of MSI tumors.
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Affiliation(s)
- Woong Na
- Department of Pathology, H Plus Yangji Hospital, Seoul, South Korea
- Department of Pathology, College of Medicine, Hanyang University, Seoul, South Korea
| | - Il Ju Lee
- Department of Biomedical Informatics, Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, South Korea
| | - Insong Koh
- Department of Biomedical Informatics, Graduate School of Biomedical Science & Engineering, Hanyang University, Seoul, South Korea
| | - Mihye Kwon
- Department of Internal Medicine, College of Medicine, Konyang University, Daejeon, South Korea
| | - Young Soo Song
- Department of Pathology, College of Medicine, Konyang University, Daejeon, South Korea
| | - Sung Hak Lee
- Department of Pathology, College of Medicine, Catholic University, Seoul, South Korea
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9
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Zhang S, Jiang R, Yang M, Wang T, Chen H, Shi Y, Liu W, Huang M. Identification of a novel eighteen-gene signature of recurrent metastasis neuroblastoma. J Mol Med (Berl) 2023; 101:403-417. [PMID: 36856811 DOI: 10.1007/s00109-023-02299-3] [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: 08/30/2022] [Revised: 01/26/2023] [Accepted: 02/14/2023] [Indexed: 03/02/2023]
Abstract
Neuroblastoma is the most common malignant tumor in childhood, and metastases occur in more than 30% patients. Recurrent metastasis is the main cause of poor prognosis and high mortality in neuroblastoma. In this regard, there is still a lack of sufficient biomarkers and effective therapies. Therefore, we performed a multi-omics analysis of neuroblastoma patients from Therapeutically Applicable Research To Generate Effective Treatments (TARGET). With clinical relapse site information, tumor samples derived from the primary site were divided into recurrent metastasis and primary tumor groups. The initial gene signature was obtained by comparing RNA-Seq and copy number variation differences. Survival data was used to further filter prognosis-related genes. This 18-gene signature consists of three clusters: tumor suppression, cell proliferation, and immunity. A super enhancer is involved in the enhanced expression of NCAPG in cluster2 together with IRF3. Based on the gene signature expression in primary neuroblastoma, it is possible to predict tumor metastasis before it occurs. According to the anticancer drug dataset of Genomics of Drug Sensitivity in Cancer (GDSC), vinorelbine and docetaxel were predicted to have high sensitivity against recurrent metastatic neuroblastoma. In conclusion, our study offers a novel metastasis biomarker and helps understand the mechanisms of tumor recurrent metastasis. KEY MESSAGES: We identified a novel eighteen-gene signature of recurrent metastasis neuroblastoma and build risk and classification models. We dissected the regulatory role of NCAPG in signatures. We found immune exhaustion and immunosuppression in recurrent metastasis neuroblastoma. Vinorelbine and docetaxel were predicted to have high sensitivity against recurrent metastatic neuroblastoma.
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Affiliation(s)
- Shufan Zhang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Rong Jiang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Manqiu Yang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Tao Wang
- Cambridge-Suda Genomic Research Center, Soochow University, Suzhou, 215123, China
| | - Hui Chen
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, 138672, Singapore
| | - Yifan Shi
- The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
| | - Wei Liu
- The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
| | - Moli Huang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, 215123, China.
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10
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Li H, Gigi L, Zhao D. CHD1, a multifaceted epigenetic remodeler in prostate cancer. Front Oncol 2023; 13:1123362. [PMID: 36776288 PMCID: PMC9909554 DOI: 10.3389/fonc.2023.1123362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/11/2023] [Indexed: 01/27/2023] Open
Abstract
Chromatin remodeling proteins contribute to DNA replication, transcription, repair, and recombination. The chromodomain helicase DNA-binding (CHD) family of remodelers plays crucial roles in embryonic development, hematopoiesis, and neurogenesis. As the founding member, CHD1 is capable of assembling nucleosomes, remodeling chromatin structure, and regulating gene transcription. Dysregulation of CHD1 at genetic, epigenetic, and post-translational levels is common in malignancies and other human diseases. Through interacting with different genetic alterations, CHD1 possesses the capabilities to exert oncogenic or tumor-suppressive functions in context-dependent manners. In this Review, we summarize the biochemical properties and dysregulation of CHD1 in cancer cells, and then discuss CHD1's roles in different contexts of prostate cancer, with an emphasis on its crosstalk with diverse signaling pathways. Furthermore, we highlight the potential therapeutic strategies for cancers with dysregulated CHD1. At last, we discuss current research gaps in understanding CHD1's biological functions and molecular basis during disease progression, as well as the modeling systems for biology study and therapeutic development.
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Affiliation(s)
- Haoyan Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
| | - Loraine Gigi
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
- Texas A&M School of Public Health, Texas A&M University, College Station, TX, United States
| | - Di Zhao
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, United States
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11
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Zhao D, Zhang M, Huang S, Liu Q, Zhu S, Li Y, Jiang W, Kiss DL, Cao Q, Zhang L, Chen K. CHD6 promotes broad nucleosome eviction for transcriptional activation in prostate cancer cells. Nucleic Acids Res 2022; 50:12186-12201. [PMID: 36408932 PMCID: PMC9757051 DOI: 10.1093/nar/gkac1090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/19/2022] [Indexed: 11/22/2022] Open
Abstract
Despite being a member of the chromodomain helicase DNA-binding protein family, little is known about the exact role of CHD6 in chromatin remodeling or cancer disease. Here we show that CHD6 binds to chromatin to promote broad nucleosome eviction for transcriptional activation of many cancer pathways. By integrating multiple patient cohorts for bioinformatics analysis of over a thousand prostate cancer datasets, we found CHD6 expression elevated in prostate cancer and associated with poor prognosis. Further comprehensive experiments demonstrated that CHD6 regulates oncogenicity of prostate cancer cells and tumor development in a murine xenograft model. ChIP-Seq for CHD6, along with MNase-Seq and RNA-Seq, revealed that CHD6 binds on chromatin to evict nucleosomes from promoters and gene bodies for transcriptional activation of oncogenic pathways. These results demonstrated a key function of CHD6 in evicting nucleosomes from chromatin for transcriptional activation of prostate cancer pathways.
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Affiliation(s)
- Dongyu Zhao
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Min Zhang
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Shaodong Huang
- Department of Biomedical Informatics, MOE Key Lab of Cardiovascular Sciences, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Qi Liu
- Department of Urology, and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Sen Zhu
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Yanqiang Li
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Weihua Jiang
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Daniel L Kiss
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Qi Cao
- Center for Inflammation and Epigenetics, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Urology, and Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Lili Zhang
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Kaifu Chen
- Prostate Cancer Program, Dana-Farber and Harvard Cancer Center, Harvard University, Boston, MA 02115, USA
- Basic and Translational Research Division, Department of Cardiology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Cardiovascular Sciences, Houston Methodist Research Institute, Houston, TX 77030, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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12
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Li X, Huo X, Zhao C, Chen Z, Xu Z, Yu J, Sun X. A novel chromatin regulator signature predicts the prognosis, clinical features and immunotherapy of colon cancer. Epigenomics 2022; 14:1325-1341. [PMID: 36545887 DOI: 10.2217/epi-2022-0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Aim: To elucidate the potential function and prognostic value of chromatin regulators (CRs) in colon cancer. Materials & methods: A comprehensive analysis of CR RNA expression data from public databases was conducted. Results: The authors successfully established and validated a 17 CR-based signature using public databases. Ten CRs of the signature were eventually verified at the protein level using the Human Protein Atlas database. Functional enrichment showed that CRs were significantly enriched in cancer-related pathways. This signature was remarkably relevant to immune cell infiltration, immune checkpoints, tumor immune dysfunction and exclusion (TIDE) score and drug sensitivity. Conclusion: The authors identified a novel, reliable prognostic signature for colon cancer. The study provided new insights into the function of CRs and has important clinical implications for immunotherapy for colon cancer.
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Affiliation(s)
- Xiaopeng Li
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xiongwei Huo
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Chenye Zhao
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Zilu Chen
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Zhengshui Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710004, China
| | - Junhui Yu
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Xuejun Sun
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
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13
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Kim N, Kim S, Song Y, Choi I, Lee SY, Kim KM, Rhu HC, Lee JY, Seo HR. Chromenopyrimidinone exhibit antitumor effects through inhibition of CAP1 (Adenylyl cyclase-associated protein 1) expression in hepatocellular carcinoma. Chem Biol Interact 2022; 365:110066. [PMID: 35931200 DOI: 10.1016/j.cbi.2022.110066] [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: 03/29/2022] [Revised: 07/05/2022] [Accepted: 07/19/2022] [Indexed: 11/03/2022]
Abstract
Hepatocellular carcinoma (HCC) is one of the most malignant human cancers, with a high mortality rate worldwide. Within an HCC tumor, cancer stem cells (CSCs) are responsible for tumor maintenance and progression and may contribute to resistance to standard HCC treatments. Previously, we characterized CD133+ cells as CSCs in primary HCC and identified chromenopyrimidinone (CPO) as a novel therapeutic for the effective treatment of CD133+ HCC. However, the biological function and molecular mechanism of CD133 remain unclear. Epigenetic alterations of CSCs have impacts on tumor initiation, progression, and therapeutic response. Here, we found that pharmacological and genetic depletion of CD133 in HCC attenuated the activity of DNA methyltransferases via control of DNMT3B stabilization. Genes were ranked by degree of promoter hypo/hyper methylation and significantly differential expression to create an "epigenetically activated by CPO" ranked genes list. Through this epigenetic analysis, we found that CPO treatment altered DNA methylation-mediated oncogenic signaling in HCCs. Specifically, CPO treatment inhibited Adenylyl cyclase-associated protein 1 (CAP1) expression, thereby reducing FAK/ERK activity and EMT-related proteins in HCC. Moreover, CPO improved the efficacy of sorafenib by inhibiting CAP1 expression and FAK/ERK activation in sorafenib-resistant HCC. These novel mechanistic insights may ultimately open up avenues for strategies targeting DNA methylation in liver cancer stem cells and provides novel therapeutic function of CPO for the effective treatment of sorafenib-resistant HCC.
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Affiliation(s)
- Namjeong Kim
- Advanced Biomedical Research Laboratory, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, South Korea
| | - Sanghwa Kim
- Advanced Biomedical Research Laboratory, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, South Korea
| | - Yeonhwa Song
- Advanced Biomedical Research Laboratory, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, South Korea
| | - Inhee Choi
- Medicinal Chemistry, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, South Korea
| | - Su-Yeon Lee
- Advanced Biomedical Research Laboratory, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, South Korea
| | - Kang Mo Kim
- Department of Gastroenterology, Asan Liver Center, Asan Medical Center, University of Ulsan College of Medicine, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, South Korea
| | - Hyung Chul Rhu
- R&D Center, J2H Biotech, Saneop-ro 156 Beon-gil, Gwonseon-gu, Suwon-si, Gyeonggi-do, 16648, Republic of Korea
| | - Ju Young Lee
- R&D Center, J2H Biotech, Saneop-ro 156 Beon-gil, Gwonseon-gu, Suwon-si, Gyeonggi-do, 16648, Republic of Korea
| | - Haeng Ran Seo
- Advanced Biomedical Research Laboratory, Institut Pasteur Korea, 16, Daewangpangyo-ro 712 Beon-gil, Bundang-gu, Seongnam-si, Gyeonggi-do, 463-400, South Korea.
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14
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Xu L, Shao F, Luo T, Li Q, Tan D, Tan Y. Pan-Cancer Analysis Identifies CHD5 as a Potential Biomarker for Glioma. Int J Mol Sci 2022; 23:ijms23158489. [PMID: 35955624 PMCID: PMC9369136 DOI: 10.3390/ijms23158489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/19/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
The chromodomain helicase DNA binding domain 5 (CHD5) is required for neural development and plays an important role in the regulation of gene expression. Although CHD5 exerts a broad tumor suppressor effect in many tumor types, its specific functions regarding its expression levels, and impact on immune cell infiltration, proliferation and migration in glioma remain unclear. Here, we evaluated the role of CHD5 in tumor immunity in a pan-cancer multi-database using the R language. The Cancer Genome Atlas (TCGA), Genotype Tissue Expression (GTEx), and Cancer Cell Lines Encyclopedia (CCLE) datasets were utilized to determine the role of CHD5 in 33 types of cancers, including the expression level, prognosis, tumor progression, and immune microenvironment. Furthermore, we explored the effect of CHD5 on glioma proliferation and migration using the cell counting kit 8 (CCK-8) assay, transwell assays and western blot analysis. The findings from our pan-cancer analysis showed that CHD5 was differentially expressed in the tumor tissues as compared to the normal tissues. Survival analysis showed that CHD5 was generally associated with the prognosis of glioblastoma (GBM), low Grade Glioma (LGG) and neuroblastoma, where the low expression of CHD5 was associated with a worse prognosis in glioma patients. Then, we confirmed that the expression level of CHD5 was associated with tumor immune infiltration and tumor microenvironment, especially in glioma. Moreover, si-RNA mediated knockdown of CHD5 promoted the proliferation and migration of glioma cells in vitro. In conclusion, CHD5 was found to be differentially expressed in the pan-cancer analysis and might play an important role in antitumor immunity. CHD5 is expected to be a potential tumor prognostic marker, especially in glioma.
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Affiliation(s)
- Lei Xu
- Laboratory Animal Center, Chongqing Medical University, Chongqing 400016, China; (L.X.); (T.L.); (Q.L.); (D.T.)
| | - Fengling Shao
- The Ministry of Education Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, China;
| | - Tengling Luo
- Laboratory Animal Center, Chongqing Medical University, Chongqing 400016, China; (L.X.); (T.L.); (Q.L.); (D.T.)
| | - Qijun Li
- Laboratory Animal Center, Chongqing Medical University, Chongqing 400016, China; (L.X.); (T.L.); (Q.L.); (D.T.)
| | - Dongmei Tan
- Laboratory Animal Center, Chongqing Medical University, Chongqing 400016, China; (L.X.); (T.L.); (Q.L.); (D.T.)
| | - Yi Tan
- Laboratory Animal Center, Chongqing Medical University, Chongqing 400016, China; (L.X.); (T.L.); (Q.L.); (D.T.)
- Correspondence:
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15
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Kuick CH, Tan JY, Jasmine D, Sumanty T, Ng AYJ, Venkatesh B, Chen H, Loh E, Jain S, Seow WY, Ng EHQ, Lian DWQ, Soh SY, Chang KTE, Chen ZX, Loh AHP. Mutations of 1p genes do not consistently abrogate tumor suppressor functions in 1p-intact neuroblastoma. BMC Cancer 2022; 22:717. [PMID: 35768791 PMCID: PMC9245282 DOI: 10.1186/s12885-022-09800-0] [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: 11/25/2021] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
Background Deletion of 1p is associated with poor prognosis in neuroblastoma, however selected 1p-intact patients still experience poor outcomes. Since mutations of 1p genes may mimic the deleterious effects of chromosomal loss, we studied the incidence, spectrum and effects of mutational variants in 1p-intact neuroblastoma. Methods We characterized the 1p status of 325 neuroblastoma patients, and correlated the mutational status of 1p tumor suppressors and neuroblastoma candidate genes with survival outcomes among 100 1p-intact cases, then performed functional validation of selected novel variants of 1p36 genes identified from our patient cohort. Results Among patients with adverse disease characteristics, those who additionally had 1p deletion had significantly worse overall survival. Among 100 tumor-normal pairs sequenced, somatic mutations of 1p tumor suppressors KIF1Bβ and CHD5 were most frequent (2%) after ALK and ATRX (8%), and BARD1 (3%). Mutations of neuroblastoma candidate genes were associated with other synchronous mutations and concurrent 11q deletion (P = 0.045). In total, 24 of 38 variants identified were novel and predicted to be deleterious or pathogenic. Functional validation identified novel KIF1Bβ I1355M variant as a gain-of-function mutation with increased expression and tumor suppressive activity, correlating with indolent clinical behavior; another novel variant CHD5 E43Q was a loss-of-function mutation with decreased expression and increased long-term cell viability, corresponding with aggressive disease characteristics. Conclusions Our study showed that chromosome 1 gene mutations occurred frequently in 1p-intact neuroblastoma, but may not consistently abrogate the function of bonafide 1p tumor suppressors. These findings may augment the evolving model of compounding contributions of 1p gene aberrations toward tumor suppressor inactivation in neuroblastoma. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-022-09800-0.
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Affiliation(s)
- Chik Hong Kuick
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Jia Ying Tan
- Neurodevelopment and Cancer Laboratory, NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Deborah Jasmine
- Neurodevelopment and Cancer Laboratory, NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Tohari Sumanty
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673, Singapore
| | - Alvin Y J Ng
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673, Singapore
| | - Byrrappa Venkatesh
- Comparative and Medical Genomics Laboratory, Institute of Molecular and Cell Biology, A*STAR, Singapore, 138673, Singapore
| | - Huiyi Chen
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Eva Loh
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Sudhanshi Jain
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Wan Yi Seow
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Eileen H Q Ng
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Derrick W Q Lian
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore
| | - Shui Yen Soh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, 229899, Singapore.,Department of Paediatric Subspecialties Haematology Oncology Service, KK Women's and Children's Hospital, Singapore, 229899, Singapore.,Duke NUS Medical School, Singapore, 169857, Singapore
| | - Kenneth T E Chang
- Department of Pathology and Laboratory Medicine, KK Women's and Children's Hospital, Singapore, 229899, Singapore.,VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, 229899, Singapore.,Duke NUS Medical School, Singapore, 169857, Singapore
| | - Zhi Xiong Chen
- Neurodevelopment and Cancer Laboratory, NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore. .,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore. .,VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,National University Cancer Institute, Singapore, 119074, Singapore.
| | - Amos H P Loh
- VIVA-KKH Paediatric Brain and Solid Tumour Programme, Children's Blood and Cancer Centre, KK Women's and Children's Hospital, Singapore, 229899, Singapore. .,Duke NUS Medical School, Singapore, 169857, Singapore. .,Department of Paediatric Surgery, KK Women's and Children's Hospital, Singapore, 229899, Singapore.
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16
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Trujillo JT, Long J, Aboelnour E, Ogas J, Wisecaver JH. CHD chromatin remodeling protein diversification yields novel clades and domains absent in classic model organisms. Genome Biol Evol 2022; 14:6582301. [PMID: 35524943 PMCID: PMC9113485 DOI: 10.1093/gbe/evac066] [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] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
Chromatin remodelers play a fundamental role in the assembly of chromatin, regulation of transcription, and DNA repair. Biochemical and functional characterizations of the CHD family of chromatin remodelers from a variety of model organisms have shown that these remodelers participate in a wide range of activities. However, because the evolutionary history of CHD homologs is unclear, it is difficult to predict which of these activities are broadly conserved and which have evolved more recently in individual eukaryotic lineages. Here, we performed a comprehensive phylogenetic analysis of 8,042 CHD homologs from 1,894 species to create a model for the evolution of this family across eukaryotes with a particular focus on the timing of duplications that gave rise to the diverse copies observed in plants, animals, and fungi. Our analysis confirms that the three major subfamilies of CHD remodelers originated in the eukaryotic last common ancestor, and subsequent losses occurred independently in different lineages. Improved taxon sampling identified several subfamilies of CHD remodelers in plants that were absent or highly divergent in the model plant Arabidopsis thaliana. Whereas the timing of CHD subfamily expansions in vertebrates corresponds to whole genome duplication events, the mechanisms underlying CHD diversification in land plants appear more complicated. Analysis of protein domains reveals that CHD remodeler diversification has been accompanied by distinct transitions in domain architecture, contributing to the functional differences observed between these remodelers. This study demonstrates the importance of proper taxon sampling when studying ancient evolutionary events to prevent misinterpretation of subsequent lineage-specific changes and provides an evolutionary framework for functional and comparative analysis of this critical chromatin remodeler family across eukaryotes.
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Affiliation(s)
- Joshua T Trujillo
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jiaxin Long
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Erin Aboelnour
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA.,Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Joseph Ogas
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jennifer H Wisecaver
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
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17
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Khaleel A, Alkhawaja B, Al-Qaisi TS, Alshalabi L, Tarkhan AH. Pathway analysis of smoking-induced changes in buccal mucosal gene expression. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022; 23:69. [PMID: 37521848 PMCID: PMC8929449 DOI: 10.1186/s43042-022-00268-y] [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: 09/10/2021] [Accepted: 02/16/2022] [Indexed: 11/10/2022] Open
Abstract
Background Cigarette smoking is the leading preventable cause of death worldwide, and it is the most common cause of oral cancers. This study aims to provide a deeper understanding of the molecular pathways in the oral cavity that are altered by exposure to cigarette smoke. Methods The gene expression dataset (accession number GSE8987, GPL96) of buccal mucosa samples from smokers (n = 5) and never smokers (n = 5) was downloaded from The National Center for Biotechnology Information's (NCBI) Gene Expression Omnibus (GEO) repository. Differential expression was ascertained via NCBI's GEO2R software, and Ingenuity Pathway Analysis (IPA) software was used to perform a pathway analysis. Results A total of 459 genes were found to be significantly differentially expressed in smoker buccal mucosa (p < 0.05). A total of 261 genes were over-expressed while 198 genes were under-expressed. The top canonical pathways predicted by IPA were nitric oxide and reactive oxygen production at macrophages, macrophages/fibroblasts and endothelial cells in rheumatoid arthritis, and thyroid cancer pathways. The IPA upstream analysis predicted that the TP53, APP, SMAD3, and TNF proteins as well as dexamethasone drug would be top transcriptional regulators. Conclusions IPA highlighted critical pathways of carcinogenesis, mainly nitric oxide and reactive oxygen production at macrophages, and confirmed widespread injury in the buccal mucosa due to exposure to cigarette smoke. Our findings suggest that cigarette smoking significantly impacts gene pathways in the buccal mucosa and may highlight potential targets for treating the effects of cigarette smoking. Supplementary Information The online version contains supplementary material available at 10.1186/s43042-022-00268-y.
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Affiliation(s)
- Anas Khaleel
- Department of Pharmacology and Biomedical Sciences, Faculty of Pharmacy and Medical Sciences, University of Petra, Amman, Jordan
| | - Bayan Alkhawaja
- Department of Pharmaceutical Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy and Medical Sciences, University of Petra, Amman, Jordan
| | - Talal Salem Al-Qaisi
- Department of Medical Laboratory Sciences, Pharmacological and Diagnostic Research Centre, Faculty of Allied Medical Sciences, Al-Ahliyya Amman University, Amman, Jordan
| | - Lubna Alshalabi
- Department of Pharmaceutical Medicinal Chemistry and Pharmacognosy, Faculty of Pharmacy and Medical Sciences, University of Petra, Amman, Jordan
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18
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Laut AK, Dorneburg C, Fürstberger A, Barth TFE, Kestler HA, Debatin KM, Beltinger C. CHD5 inhibits metastasis of neuroblastoma. Oncogene 2022; 41:622-633. [PMID: 34789839 PMCID: PMC8799470 DOI: 10.1038/s41388-021-02081-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 11/09/2022]
Abstract
CHD5, a tumor suppressor at 1p36, is frequently lost or silenced in poor prognosis neuroblastoma (NB) and many adult cancers. The role of CHD5 in metastasis is unknown. We confirm that low expression of CHD5 is associated with stage 4 NB. Forced expression of CHD5 in NB cell lines with 1p loss inhibited key aspects of the metastatic cascade in vitro: anchorage-independent growth, migration, and invasion. In vivo, formation of bone marrow and liver metastases developing from intravenously injected NB cells was delayed and decreased by forced CHD5 expression. Genome-wide mRNA sequencing revealed reduction of genes and gene sets associated with metastasis when CHD5 was overexpressed. Known metastasis-suppressing genes preferentially upregulated in CHD5-overexpressing NB cells included PLCL1. In patient NB, low expression of PLCL1was associated with metastatic disease and poor survival. Knockdown of PLCL1 and of p53 in IMR5 NB cells overexpressing CHD5 reversed CHD5-induced inhibition of invasion and migration in vitro. In summary, CHD5 is a metastasis suppressor in NB.
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Affiliation(s)
- Astrid K Laut
- Section Experimental Pediatric Oncology, Dept. of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Carmen Dorneburg
- Section Experimental Pediatric Oncology, Dept. of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Axel Fürstberger
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | | | - Hans A Kestler
- Institute of Medical Systems Biology, Ulm University, Ulm, Germany
| | - Klaus-Michael Debatin
- Dept. of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Christian Beltinger
- Section Experimental Pediatric Oncology, Dept. of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany.
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19
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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20
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Liu C, Kang N, Guo Y, Gong P. Advances in Chromodomain Helicase DNA-Binding (CHD) Proteins Regulating Stem Cell Differentiation and Human Diseases. Front Cell Dev Biol 2021; 9:710203. [PMID: 34616726 PMCID: PMC8488160 DOI: 10.3389/fcell.2021.710203] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 07/29/2021] [Indexed: 12/15/2022] Open
Abstract
Background: Regulation of gene expression is critical for stem cell differentiation, tissue development, and human health maintenance. Recently, epigenetic modifications of histone and chromatin remodeling have been verified as key controllers of gene expression and human diseases. Objective: In this study, we review the role of chromodomain helicase DNA-binding (CHD) proteins in stem cell differentiation, cell fate decision, and several known human developmental disorders and cancers. Conclusion: CHD proteins play a crucial role in stem cell differentiation and human diseases.
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Affiliation(s)
- Caojie Liu
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Ning Kang
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Yuchen Guo
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
| | - Ping Gong
- State Key Laboratory of Oral Diseases, West China School of Stomatology, Sichuan University, Chengdu, China
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21
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Johann PD. Invited Review: Dysregulation of chromatin remodellers in paediatric brain tumours - SMARCB1 and beyond. Neuropathol Appl Neurobiol 2021; 46:57-72. [PMID: 32307752 DOI: 10.1111/nan.12616] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/21/2020] [Indexed: 12/13/2022]
Abstract
Mutations in chromatin remodelling genes occur in approximately 25% of all human tumours (Kadoch et al. Nat Genet 45: 592-601, 2013). The spectrum of alterations is broad and comprises single nucleotide variants, insertion/deletions and more complex structural variations. The single most often affected remodelling complex is the SWI/SNF complex (SWItch/sucrose non-fermentable). In the field of paediatric neuro-oncology, the spectrum of affected genes implicated in epigenetic remodelling is narrower with SMARCB1 and SMARCA4 being the most frequent. The low mutation frequencies in many of the SWI/SNF mutant entities underline the fact that perturbed chromatin remodelling is the most salient factor in tumourigenesis and could thus be a potential therapeutic opportunity. Here, I review the genetic basis of aberrant chromatin remodelling in paediatric brain tumours and discuss their impact on the epigenome in the respective entities, mainly medulloblastomas and rhabdoid tumours.
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Affiliation(s)
- P D Johann
- Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany.,Division of Paediatric Neurooncology, German Cancer Research Center (DKFZ) and German Cancer Research Consortium (DKTK), Heidelberg, Germany.,Department of Paediatric Haematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
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22
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Wilson MM, Henshall DC, Byrne SM, Brennan GP. CHD2-Related CNS Pathologies. Int J Mol Sci 2021; 22:E588. [PMID: 33435571 PMCID: PMC7827033 DOI: 10.3390/ijms22020588] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/04/2021] [Accepted: 01/05/2021] [Indexed: 02/08/2023] Open
Abstract
Epileptic encephalopathies (EE) are severe epilepsy syndromes characterized by multiple seizure types, developmental delay and even regression. This class of disorders are increasingly being identified as resulting from de novo genetic mutations including many identified mutations in the family of chromodomain helicase DNA binding (CHD) proteins. In particular, several de novo pathogenic mutations have been identified in the gene encoding chromodomain helicase DNA binding protein 2 (CHD2), a member of the sucrose nonfermenting (SNF-2) protein family of epigenetic regulators. These mutations in the CHD2 gene are causative of early onset epileptic encephalopathy, abnormal brain function, and intellectual disability. Our understanding of the mechanisms by which modification or loss of CHD2 cause this condition remains poorly understood. Here, we review what is known and still to be elucidated as regards the structure and function of CHD2 and how its dysregulation leads to a highly variable range of phenotypic presentations.
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Affiliation(s)
- Marc-Michel Wilson
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland; (M.-M.W.); (D.C.H.)
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
| | - David C. Henshall
- Department of Physiology and Medical Physics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland; (M.-M.W.); (D.C.H.)
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
| | - Susan M. Byrne
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
- Department of Paediatrics, RCSI, University of Medicine and Health Sciences, Dublin 02, Ireland
- Department of Paediatric Neurology, Our Ladies Children’s Hospital Crumlin, Dublin 12, Ireland
| | - Gary P. Brennan
- FutureNeuro SFI Research Centre, RCSI, University of Medicine and Health Sciences, Dublin D02 YN77, Ireland;
- UCD School of Biomolecular and Biomedical Science, UCD Conway Institute, University College Dublin, Belfield, Dublin 04, Ireland
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23
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Pei S, Chen Z, Tan H, Fan L, Zhang B, Zhao C. SLC16A1-AS1 enhances radiosensitivity and represses cell proliferation and invasion by regulating the miR-301b-3p/CHD5 axis in hepatocellular carcinoma. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:42778-42790. [PMID: 32748357 DOI: 10.1007/s11356-020-09998-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 07/02/2020] [Indexed: 06/11/2023]
Abstract
Hepatocellular carcinoma (HCC), a common type of human malignancies, leads to increasing incidence and fairly high mortality. An increasing number of studies have verified that long noncoding RNAs (lncRNAs) played key roles in the development of multiple human cancers. As a biomarker, SLC16A1-AS1 has been reported in non-small cell lung cancer (NSCLC) and oral squamous cell carcinoma (OSCC). Thus, we decided to investigate whether SLC16A1-AS1 exerts its biological function in HCC. In this study, we discovered that SLC16A1-AS1 was obviously downregulated in HCC tissues and cells. Overexpression of SLC16A1-AS1 inhibited HCC cell proliferation, invasion, and epithelial-mesenchymal transition (EMT) process as well as promoted cell apoptosis. Moreover, SLC16A1-AS1 was confirmed to enhance the radiosensitivity of HCC cells. Molecular mechanism exploration suggested that SLC16A1-AS1 served as a sponge for miR-301b-3p and CHD5 was the downstream target gene of miR-301b-3p in HCC cells. Rescue assays implied that CHD5 knockdown could recover the effects of SLC16A1-AS1 overexpression on HCC cellular processes. In brief, our study clarified that SLC16A1-AS1 acted as a tumor suppressor in HCC by targeting the miR-301b-3p/CHD5 axis, which may be a promising diagnostic biomarker and provide promising treatment for HCC patients.
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Affiliation(s)
- Shenglin Pei
- Department of Anesthesiology, Affiliated Tumor Hospital of Guangxi Medical University, Nanning, China
| | - Zuyi Chen
- Department of Intervention, Affiliated Tumor Hospital of Guangxi Medical University, No. 71 Hedi Road, Qingxiu District, Nanning, 530021, Guangxi, China
| | - Huajun Tan
- Department of Intervention, Affiliated Tumor Hospital of Guangxi Medical University, No. 71 Hedi Road, Qingxiu District, Nanning, 530021, Guangxi, China
| | - Liwei Fan
- Department of Intervention, Affiliated Tumor Hospital of Guangxi Medical University, No. 71 Hedi Road, Qingxiu District, Nanning, 530021, Guangxi, China
| | - Baina Zhang
- Department of Intervention, Affiliated Tumor Hospital of Guangxi Medical University, No. 71 Hedi Road, Qingxiu District, Nanning, 530021, Guangxi, China
| | - Chang Zhao
- Department of Intervention, Affiliated Tumor Hospital of Guangxi Medical University, No. 71 Hedi Road, Qingxiu District, Nanning, 530021, Guangxi, China.
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24
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Campos Cogo S, Gradowski Farias da Costa do Nascimento T, de Almeida Brehm Pinhatti F, de França Junior N, Santos Rodrigues B, Regina Cavalli L, Elifio-Esposito S. An overview of neuroblastoma cell lineage phenotypes and in vitro models. Exp Biol Med (Maywood) 2020; 245:1637-1647. [PMID: 32787463 PMCID: PMC7802384 DOI: 10.1177/1535370220949237] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
This review was conducted to present the main neuroblastoma (NB) clinical characteristics and the most common genetic alterations present in these pediatric tumors, highlighting their impact in tumor cell aggressiveness behavior, including metastatic development and treatment resistance, and patients' prognosis. The distinct three NB cell lineage phenotypes, S-type, N-type, and I-type, which are characterized by unique cell surface markers and gene expression patterns, are also reviewed. Finally, an overview of the most used NB cell lines currently available for in vitro studies and their unique cellular and molecular characteristics, which should be taken into account for the selection of the most appropriate model for NB pre-clinical studies, is presented. These valuable models can be complemented by the generation of NB reprogrammed tumor cells or organoids, derived directly from patients' tumor specimens, in the direction toward personalized medicine.
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Affiliation(s)
- Sheron Campos Cogo
- Graduate Program in Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba 80215-901, Brazil
| | | | | | - Nilton de França Junior
- Graduate Program in Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba 80215-901, Brazil
| | - Bruna Santos Rodrigues
- Graduate Program in Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba 80215-901, Brazil
| | - Luciane Regina Cavalli
- Instituto de Pesquisa Pelé Pequeno Príncipe, Faculdades Pequeno Príncipe, Curitiba 80250-060, Brazil
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20007, USA
| | - Selene Elifio-Esposito
- Graduate Program in Health Sciences, Pontifícia Universidade Católica do Paraná, Curitiba 80215-901, Brazil
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25
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The mechanisms of action of chromatin remodelers and implications in development and disease. Biochem Pharmacol 2020; 180:114200. [DOI: 10.1016/j.bcp.2020.114200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
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26
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Chromodomain Helicase DNA-Binding Protein 5 Inhibits Renal Cell Carcinoma Tumorigenesis by Activation of the p53 and RB Pathways. BIOMED RESEARCH INTERNATIONAL 2020; 2020:5425612. [PMID: 33062682 PMCID: PMC7542531 DOI: 10.1155/2020/5425612] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/15/2020] [Accepted: 08/05/2020] [Indexed: 12/24/2022]
Abstract
Chromodomain helicase DNA-binding protein 5 (CHD5) plays a crucial tumor suppressor role in multiple types of tumors. For this study, we investigated its clinical significance and the molecular mechanism(s) underlying tumorigenesis in renal cell carcinoma (RCC). Initially, CHD5 expression was assessed in primary tumor tissue and in tissue array. Correlations among CHD5 expression and clinicopathological characteristics were analyzed. Next, lentivirus-mediated CHD5 overexpression in the ACHN and 769-P cells was used to assess effects on proliferation, migration, invasion ability, and the regulation of the p14ARF/p53 and p16INK4a/RB signaling pathways. Finally, a xenograft mouse model was used to verify its impact on tumor growth in vivo. Results demonstrated that CHD5 was downregulated in tumor tissues and that low CHD5 expression was correlated with advanced TNM stage, high Fuhrman grade, lymph node metastasis, and poor survival. Overexpression of CHD5 inhibited proliferation, migration, and invasion in vitro; prompted cell cycle G1 phase arrest; induced apoptosis; and suppressed tumor growth in vivo. Furthermore, we confirmed that CHD5 activates the p53 and RB pathways to inhibit tumorigenesis in RCC. In summary, CHD5 is involved in the initiation and progression of RCC and may serve as a diagnostic biomarker and a potential therapeutic target for RCC.
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27
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Advani D, Gupta R, Tripathi R, Sharma S, Ambasta RK, Kumar P. Protective role of anticancer drugs in neurodegenerative disorders: A drug repurposing approach. Neurochem Int 2020; 140:104841. [PMID: 32853752 DOI: 10.1016/j.neuint.2020.104841] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/24/2020] [Accepted: 08/18/2020] [Indexed: 12/13/2022]
Abstract
The disease heterogeneity and little therapeutic progress in neurodegenerative diseases justify the need for novel and effective drug discovery approaches. Drug repurposing is an emerging approach that reinvigorates the classical drug discovery method by divulging new therapeutic uses of existing drugs. The common biological background and inverse tuning between cancer and neurodegeneration give weight to the conceptualization of repurposing of anticancer drugs as novel therapeutics. Many studies are available in the literature, which highlights the success story of anticancer drugs as repurposed therapeutics. Among them, kinase inhibitors, developed for various oncology indications evinced notable neuroprotective effects in neurodegenerative diseases. In this review, we shed light on the salient role of multiple protein kinases in neurodegenerative disorders. We also proposed a feasible explanation of the action of kinase inhibitors in neurodegenerative disorders with more attention towards neurodegenerative disorders. The problem of neurotoxicity associated with some anticancer drugs is also highlighted. Our review encourages further research to better encode the hidden potential of anticancer drugs with the aim of developing prospective repurposed drugs with no toxicity for neurodegenerative disorders.
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Affiliation(s)
- Dia Advani
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Rohan Gupta
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Rahul Tripathi
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Sudhanshu Sharma
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Rashmi K Ambasta
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India
| | - Pravir Kumar
- Department of Biotechnology, Molecular Neuroscience and Functional Genomics Laboratory, Room# FW4TF3, Mechanical Engineering Building, Shahbad Daulatpur, Bawana Road, Delhi, 110042, India.
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28
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Machine Learning Supports Long Noncoding RNAs as Expression Markers for Endometrial Carcinoma. BIOMED RESEARCH INTERNATIONAL 2020; 2020:3968279. [PMID: 32420338 PMCID: PMC7199595 DOI: 10.1155/2020/3968279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 12/17/2019] [Indexed: 12/19/2022]
Abstract
Uterine corpus endometrial carcinoma (UCEC) is the second most common type of gynecological tumor. Several research studies have recently shown the potential of different ncRNAs as biomarkers for prognostics and diagnosis in different types of cancers, including UCEC. Thus, we hypothesized that long noncoding RNAs (lncRNAs) could serve as efficient factors to discriminate solid primary (TP) and normal adjacent (NT) tissues in UCEC with high accuracy. We performed an in silico differential expression analysis comparing TP and NT from a set of samples downloaded from the Cancer Genome Atlas (TCGA) database, targeting highly differentially expressed lncRNAs that could potentially serve as gene expression markers. All analyses were performed in R software. The receiver operator characteristics (ROC) analyses and both supervised and unsupervised machine learning indicated a set of 14 lncRNAs that may serve as biomarkers for UCEC. Functions and putative pathways were assessed through a coexpression network and target enrichment analysis.
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29
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Hashimoto T, Kurokawa Y, Wada N, Takahashi T, Miyazaki Y, Tanaka K, Makino T, Yamasaki M, Nakajima K, Mori M, Doki Y. Clinical significance of chromatin remodeling factor CHD5 expression in gastric cancer. Oncol Lett 2020; 19:1066-1073. [PMID: 31897220 PMCID: PMC6924149 DOI: 10.3892/ol.2019.11138] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 10/08/2019] [Indexed: 12/19/2022] Open
Abstract
Chromodomain helicase DNA-binding 5 (CHD5), which is a member of the CHD family, has been identified as a tumor suppressor gene in a variety of malignancies. The aim of the current study was to clarify the clinical significance of CHD5 expression in gastric cancer. CHD5 expression was evaluated using immunohistochemistry (IHC) in 154 specimens resected from patients with gastric cancer from January 2011 to December 2013, and assessed its relationships with clinicopathological characteristics and survival. In vitro cell proliferation, invasion, and migration assays and western blotting analysis were performed to clarify the role of CHD5 in human gastric cancer cell lines. Of a total of 154 patients, 57 (37.0%) exhibited low CHD5 expression, which was significantly associated with positive lymphatic invasion (P=0.032), advanced pT status (P=0.011), and advanced pStage (P=0.014). Overall survival (OS) in patients with low CHD5 expression was significantly worse compared with patients with high CHD5 expression (hazard ratio, 1.96; 95% confidence interval, 1.09-3.45; log-rank P=0.023). Cox multivariate analysis for OS revealed that CHD5 expression was an independent prognostic factor with age and pN status. In vitro, the upregulation of CHD5 in gastric cancer cells with low CHD5 expression significantly decreased cell proliferation, migration and invasion. CHD5 was associated with the regulation of multiple cancer-related targets, including p53 and enhancer of zeste homolog 2 (EZH2) in western blotting analysis. In conclusion, since CHD5 regulated multiple cancer-related targets, its expression may be a useful prognostic biomarker in patients with gastric cancer.
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Affiliation(s)
- Tadayoshi Hashimoto
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Yukinori Kurokawa
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Noriko Wada
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Tsuyoshi Takahashi
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Yasuhiro Miyazaki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Koji Tanaka
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Tomoki Makino
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Makoto Yamasaki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Kiyokazu Nakajima
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - Masaki Mori
- Department of Surgery and Science, Kyushu University Graduate School of Medical Sciences, Fukuoka 812-8582, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
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30
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Pierson TM, Otero MG, Grand K, Choi A, Graham JM, Young JI, Mackay JP. The NuRD complex and macrocephaly associated neurodevelopmental disorders. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2019; 181:548-556. [PMID: 31737996 DOI: 10.1002/ajmg.c.31752] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/08/2019] [Accepted: 10/10/2019] [Indexed: 12/13/2022]
Abstract
The nucleosome remodeling and deacetylase (NuRD) complex is a major regulator of gene expression involved in pluripotency, lineage commitment, and corticogenesis. This important complex is composed of seven different proteins, with mutations in CHD3, CHD4, and GATAD2B being associated with neurodevelopmental disorders presenting with macrocephaly and intellectual disability similar to other overgrowth and intellectual disability (OGID) syndromes. Pathogenic variants in CHD3 and CHD4 primarily involve disruption of enzymatic function. GATAD2B variants include loss-of-function mutations that alter protein dosage and missense variants that involve either of two conserved domains (CR1 and CR2) known to interact with other NuRD proteins. In addition to macrocephaly and intellectual disability, CHD3 variants are associated with inguinal hernias and apraxia of speech; whereas CHD4 variants are associated with skeletal anomalies, deafness, and cardiac defects. GATAD2B-associated neurodevelopmental disorder (GAND) has phenotypic overlap with both of these disorders. Of note, structural models of NuRD indicate that CHD3 and CHD4 require direct contact with the GATAD2B-CR2 domain to interact with the rest of the complex. Therefore, the phenotypic overlaps of CHD3- and CHD4-related disorders with GAND are consistent with a loss in the ability of GATAD2B to recruit CHD3 or CHD4 to the complex. The shared features of these neurodevelopmental disorders may represent a new class of OGID syndrome: the NuRDopathies.
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Affiliation(s)
- Tyler Mark Pierson
- Department of Pediatrics, Cedars-Sinai Medical Center, Los Angeles, California.,Department of Neurology, Cedars-Sinai Medical Center, Los Angeles, California.,Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Maria G Otero
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - Katheryn Grand
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Andrew Choi
- Board of Governors Regenerative Medicine Institute, Cedars-Sinai Medical Center, Los Angeles, California
| | - John M Graham
- Department of Pediatrics, Medical Genetics, Cedars-Sinai Medical Center, Los Angeles, California
| | - Juan I Young
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida
| | - Joel P Mackay
- School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales, Australia
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31
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Guo M, Peng Y, Gao A, Du C, Herman JG. Epigenetic heterogeneity in cancer. Biomark Res 2019; 7:23. [PMID: 31695915 PMCID: PMC6824025 DOI: 10.1186/s40364-019-0174-y] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Phenotypic and functional heterogeneity is one of the hallmarks of human cancers. Tumor genotype variations among tumors within different patients are known as interpatient heterogeneity, and variability among multiple tumors of the same type arising in the same patient is referred to as intra-patient heterogeneity. Subpopulations of cancer cells with distinct phenotypic and molecular features within a tumor are called intratumor heterogeneity (ITH). Since Nowell proposed the clonal evolution of tumor cell populations in 1976, tumor heterogeneity, especially ITH, was actively studied. Research has focused on the genetic basis of cancer, particularly mutational activation of oncogenes or inactivation of tumor-suppressor genes (TSGs). The phenomenon of ITH is commonly explained by Darwinian-like clonal evolution of a single tumor. Despite the monoclonal origin of most cancers, new clones arise during tumor progression due to the continuous acquisition of mutations. It is clear that disruption of the "epigenetic machinery" plays an important role in cancer development. Aberrant epigenetic changes occur more frequently than gene mutations in human cancers. The epigenome is at the intersection of the environment and genome. Epigenetic dysregulation occurs in the earliest stage of cancer. The current trend of epigenetic therapy is to use epigenetic drugs to reverse and/or delay future resistance to cancer therapies. A majority of cancer therapies fail to achieve durable responses, which is often attributed to ITH. Epigenetic therapy may reverse drug resistance in heterogeneous cancer. Complete understanding of genetic and epigenetic heterogeneity may assist in designing combinations of targeted therapies based on molecular information extracted from individual tumors.
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Affiliation(s)
- Mingzhou Guo
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, 40 Daxue Road, Zhengzhou, Henan 450052 China
| | - Yaojun Peng
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Aiai Gao
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Chen Du
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- 3The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Ave., Pittsburgh, PA 15213 USA
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32
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Yarrow supercritical extract exerts antitumoral properties by targeting lipid metabolism in pancreatic cancer. PLoS One 2019; 14:e0214294. [PMID: 30913248 PMCID: PMC6435158 DOI: 10.1371/journal.pone.0214294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 03/11/2019] [Indexed: 12/15/2022] Open
Abstract
Metabolic reprogramming is considered a hallmark of cancer. Currently, the altered lipid metabolism in cancer is a topic of interest due to the prominent role of lipids regulating the progression of various types of tumors. Lipids and lipid-derived molecules have been shown to activate growth regulatory pathways and to promote malignancy in pancreatic cancer. In a previous work, we have described the antitumoral properties of Yarrow (Achillea Millefolium) CO2 supercritical extract (Yarrow SFE) in pancreatic cancer. Herein, we aim to investigate the underlaying molecular mechanisms by which Yarrow SFE induces cytotoxicity in pancreatic cancer cells. Yarrow SFE downregulates SREBF1 and downstream molecular targets of this transcription factor, such as fatty acid synthase (FASN) and stearoyl-CoA desaturase (SCD). Importantly, we demonstrate the in vivo effect of Yarrow SFE diminishing the tumor growth in a xenograft mouse model of pancreatic cancer. Our data suggest that Yarrow SFE can be proposed as a complementary adjuvant or nutritional supplement in pancreatic cancer therapy.
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33
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Zhu L, Wang R, Zhang L, Zuo C, Zhang R, Zhao S. rs187960998 polymorphism in miR-211 prevents development of human colon cancer by deregulation of 3'UTR in CHD5. Onco Targets Ther 2019; 12:405-412. [PMID: 30655677 PMCID: PMC6322703 DOI: 10.2147/ott.s180935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Background Previous research indicated that overexpression of miRNA-211 could promote colorectal cancer cell growth by targeting tumor suppressive gene Chromodomain-helicase-DNA-binding protein 5 (CHD5) in human colon cancer (CC). Moreover, the function of the single-nucleotide polymorphism (SNP) located in the mature region of miR-211 has not been investigated. In this study, we found that SNP of rs187960998 in miR-211 was involved in the occurrence of CC by acting as a tumor suppressor by mal-regulation of its target gene CHD5. Materials and methods The genotype of total 685 CC patients was detected by real-time PCR, the proliferation of CC cell lines with different genotypes of miR-211 was determined by Cell Counting Kit-8, cell invasion evaluated by transwell and the activity of the CHD5 promoter in CC cell lines transfected with different miR-211 was determined by luciferase assay. The expression of CHD5 in CC patients was determined by the immunohistochemistry, and the relapse-free survival rate was analyzed by Kaplan–Meier analysis. Results C/T SNP of miR-211 could inhibit CC cell proliferation and invasion by upregulation of CHD5. And SNP in rs187960998 of miR-211 was associated with tumor size, metastasis and tumor differentiation in CC patients. Patients with CC genotype have significantly low CHD5 expression than the T-carrier, while no significant expression difference in miR-211 expression among different genotype subsets. Patients with CC genotype have significantly shorter postsurgery survival rate compared to the T-carrier. Conclusion rs187960998 in miR-211 was highly associated with a decreased risk of CC in the Chinese population by deregulating a tumor suppressive gene CHD5.
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Affiliation(s)
- Limei Zhu
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
| | - Ran Wang
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
| | - Li Zhang
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
| | - Chunlei Zuo
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
| | - Rui Zhang
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
| | - Shaolin Zhao
- Department of Clinical Laboratory, The First People's Hospital of Lianyungang, Lianyungang, Jiangsu, China,
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Han TS, Ban HS, Hur K, Cho HS. The Epigenetic Regulation of HCC Metastasis. Int J Mol Sci 2018; 19:ijms19123978. [PMID: 30544763 PMCID: PMC6321007 DOI: 10.3390/ijms19123978] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 12/05/2018] [Accepted: 12/07/2018] [Indexed: 12/22/2022] Open
Abstract
Epigenetic alterations, such as histone modification, DNA methylation, and miRNA-mediated processes, are critically associated with various mechanisms of proliferation and metastasis in several types of cancer. To overcome the side effects and limited effectiveness of drugs for cancer treatment, there is a continuous need for the identification of more effective drug targets and the execution of mechanism of action (MOA) studies. Recently, epigenetic modifiers have been recognized as important therapeutic targets for hepatocellular carcinoma (HCC) based on their reported abilities to suppress HCC metastasis and proliferation in both in vivo and in vitro studies. Therefore, here, we introduce epigenetic modifiers and alterations related to HCC metastasis and proliferation, and their molecular mechanisms in HCC metastasis. The existing data suggest that the study of epigenetic modifiers is important for the development of specific inhibitors and diagnostic targets for HCC treatment.
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Affiliation(s)
- Tae-Su Han
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
| | - Hyun Seung Ban
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
| | - Keun Hur
- Department of Biochemistry and Cell Biology, School of Medicine, Kyungpook National University, Daegu 41944, Korea.
| | - Hyun-Soo Cho
- Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea.
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35
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Zhang L, Chen Y, Jiang Q, Song W, Zhang L. Therapeutic potential of selective histone deacetylase 3 inhibition. Eur J Med Chem 2018; 162:534-542. [PMID: 30472601 DOI: 10.1016/j.ejmech.2018.10.072] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 10/18/2018] [Accepted: 10/19/2018] [Indexed: 02/06/2023]
Abstract
Histone deacetylases (HDACs) are closely related to the occurrence and development of a variety of diseases, such as tumor, inflammation, diabetes mellitus, cardiovascular and neurodegenerative diseases. Inhibition of HDACs by developing HDAC inhibitors has achieved significant progress in the treatment of diseases caused by epigenetic abnormalities, and especially in the cancer therapy. Isoform selective HDAC inhibitors are emphasized to be disease specific and have less off-target effects and better safety performances. HDAC3 has been illustrated to play specific role in the development of several diseases, and the discovery of HDAC3 selective inhibitors has exhibited potential in the targeted disease treatment. Herein, we summarize the current knowledge about the prospects of selective inhibition of HDAC3 for the drug development.
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Affiliation(s)
- Lihui Zhang
- School of Stomatology, Weifang Medical University, Weifang, Shandong, China
| | - Yiming Chen
- Department of Medicinal Chemistry, School of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Qixiao Jiang
- School of Pharmacy, Qingdao University, Qingdao, Shandong, China
| | - Weiguo Song
- Department of Medicinal Chemistry, School of Pharmacy, Weifang Medical University, Weifang, Shandong, China
| | - Lei Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Weifang Medical University, Weifang, Shandong, China.
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36
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Dai JY, Wang X, Buas MF, Zhang C, Ma J, Wei B, Li Y, Zhao B, Hyun TS, Chen X, Loeb KR, Odze R, Yao L, Sun X, Self S, Vaughan TL, Guo Y. Whole-genome sequencing of esophageal adenocarcinoma in Chinese patients reveals distinct mutational signatures and genomic alterations. Commun Biol 2018; 1:174. [PMID: 30374464 PMCID: PMC6200836 DOI: 10.1038/s42003-018-0182-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 09/25/2018] [Indexed: 12/19/2022] Open
Abstract
While the incidence of esophageal adenocarcinoma (EAC) has risen drastically in Western countries over the last 40 years, a similar trend has not been observed for EAC in China. Here, we analyzed mutational spectrum, copy number alterations, and structural variants from whole-genome sequencing of 10 Chinese EAC tumor samples and their matched normal samples, and compared them to previously reported EAC tumor specimens from Western countries. The mutational burden in Chinese EAC was significantly lower than that found in EAC from Western countries. The hallmark A>C mutational signature observed at high frequency in EAC from Western countries, which has been linked to acid reflux, is completely absent in Chinese samples. Furthermore, none of the Chinese samples showed evidence of chromothripsis and genome doubling that are often found in EAC from Western countries. In summary, Chinese EAC tumor samples had distinct genomic profiles and signatures, suggesting that EAC in Chinese individuals may arise from a different etiological pathway.
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Affiliation(s)
- James Y Dai
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA.
- Department of Biostatistics, University of Washington, Seattle, 98195, WA, USA.
| | - Xiaoyu Wang
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
| | - Matthew F Buas
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, 14203, NY, USA
| | - Chengjuan Zhang
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, He Nan Province, China
| | - Jie Ma
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, He Nan Province, China
| | - Bing Wei
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, He Nan Province, China
| | - Yin Li
- Department of Thoracic Surgery, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, He Nan Province, China
| | - Baosheng Zhao
- Department of Thoracic Surgery, The First Affiliated Hospital of Xinxiang Medical College, Xinxiang, 450008, He Nan Province, China
| | - Teresa S Hyun
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
- Department of Pathology, University of Washington, Seattle, 98195, WA, USA
| | - Xueyan Chen
- Department of Laboratory Medicine, University of Washington, Seattle, 98195, WA, USA
| | - Keith R Loeb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
- Department of Pathology, University of Washington, Seattle, 98195, WA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, 98195, WA, USA
| | - Robert Odze
- Department of Pathology, Brigham and Women's Hospital, Boston, 02115, MA, USA
| | - Lena Yao
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
| | - Xin Sun
- Institute of Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, 100050, China
| | - Steve Self
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
| | - Thomas L Vaughan
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, 98109, WA, USA
- Department of Epidemiology, University of Washington, Seattle, 98195, WA, USA
| | - Yongjun Guo
- Department of Molecular Pathology, The Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450008, He Nan Province, China.
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37
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Xiao Q, Chen L, Luo H, Li H, Kong Q, Jiao F, Pang S, Zhang M, Lan F, Fan W, Luo H, Tao T, Zhu X. A rare CHD5 haplotype and its interactions with environmental factors predicting hepatocellular carcinoma risk. BMC Cancer 2018; 18:658. [PMID: 29907144 PMCID: PMC6003142 DOI: 10.1186/s12885-018-4551-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2017] [Accepted: 05/24/2018] [Indexed: 01/10/2023] Open
Abstract
Background CHD5 is a conventional tumour-suppressing gene in many tumours. The aim of this study was to determine whether CHD5 variants contribute to the risk of hepatocellular carcinoma (HCC). Methods Gene variants were identified using next-generation sequencing targeted on referenced mutations followed by TaqMan genotyping in two case-control studies. Results We discovered a rare variant (haplotype AG) in CHD5 (rs12564469-rs9434711) that was markedly associated with the risk of HCC in a Chinese population. A logistical regression model and permutation test confirmed the association. Indeed, the association quality increased in a gene dose-dependent manner as the number of samples increased. In the stratified analysis, this haplotype risk effect was statistically significant in a subgroup of alcohol drinkers. The false-positive report probability and multifactor dimensionality reduction further supported the finding. Conclusions Our results suggest that the rare CHD5 gene haplotype and alcohol intake contribute to the risk of HCC. Our findings can be valuable to researchers of cancer precision medicine looking to improve diagnosis and treatment of HCC. Electronic supplementary material The online version of this article (10.1186/s12885-018-4551-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Qin Xiao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Department of Blood Transfusion, Peking University Shenzhen Hospital, Shenzhen, China
| | - Lianzhou Chen
- Digestive System Tumor Tissue Bank, Center of Surgery Laboratory, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haiqing Luo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,The Affiliated Hospital Cancer Center, Guangdong Medical University, Zhanjiang, China
| | - Hongmei Li
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Department of Pathology, Guangdong Medical University, Dongguan, China
| | - Qingming Kong
- Immunity and Biochemical Research Lab, Zhejiang Academy of Medical Sciences, Hangzhou, China
| | - Fei Jiao
- Department of Biochemistry and Molecular Biology, Binzhou Medical University, Yantai, China
| | - Shifeng Pang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Ming Zhang
- Department of Gastroenterology, Zibo Central Hospital, Zibo, China
| | - Feifei Lan
- Forensic Identification Institute, Guangdong Women and Children Hospital, Guangzhou, China
| | - Wenguo Fan
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Hui Luo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.
| | - Tao Tao
- Department of Gastroenterology, Zibo Central Hospital, Zibo, China.
| | - Xiao Zhu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.
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38
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Covalent Modifications of Histone H3K9 Promote Binding of CHD3. Cell Rep 2018; 21:455-466. [PMID: 29020631 DOI: 10.1016/j.celrep.2017.09.054] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 08/12/2017] [Accepted: 09/15/2017] [Indexed: 12/15/2022] Open
Abstract
Chromatin remodeling is required for genome function and is facilitated by ATP-dependent complexes, such as nucleosome remodeling and deacetylase (NuRD). Among its core components is the chromodomain helicase DNA binding protein 3 (CHD3) whose functional significance is not well established. Here, we show that CHD3 co-localizes with the other NuRD subunits, including HDAC1, near the H3K9ac-enriched promoters of the NuRD target genes. The tandem PHD fingers of CHD3 bind histone H3 tails and posttranslational modifications that increase hydrophobicity of H3K9-methylation or acetylation (H3K9me3 or H3K9ac)-enhance this interaction. Binding of CHD3 PHDs promotes H3K9Cme3-nucleosome unwrapping in vitro and perturbs the pericentric heterochromatin structure in vivo. Methylation or acetylation of H3K9 uniquely alleviates the intra-nucleosomal interaction of histone H3 tails, increasing H3K9 accessibility. Collectively, our data suggest that the targeting of covalently modified H3K9 by CHD3 might be essential in diverse functions of NuRD.
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39
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Combined HAT/EZH2 modulation leads to cancer-selective cell death. Oncotarget 2018; 9:25630-25646. [PMID: 29876013 PMCID: PMC5986654 DOI: 10.18632/oncotarget.25428] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 05/02/2018] [Indexed: 12/20/2022] Open
Abstract
Epigenetic alterations have been associated with both pathogenesis and progression of cancer. By screening of library compounds, we identified a novel hybrid epi-drug MC2884, a HAT/EZH2 inhibitor, able to induce bona fide cancer-selective cell death in both solid and hematological cancers in vitro, ex vivo and in vivo xenograft models. Anticancer action was due to an epigenome modulation by H3K27me3, H3K27ac, H3K9/14ac decrease, and to caspase-dependent apoptosis induction. MC2884 triggered mitochondrial pathway apoptosis by up-regulation of cleaved-BID, and strong down-regulation of BCL2. Even aggressive models of cancer, such as p53-/- or TET2-/- cells, responded to MC2884, suggesting MC2884 therapeutic potential also for the therapy of TP53 or TET2-deficient human cancers. MC2884 induced massive apoptosis in ex vivo human primary leukemia blasts with poor prognosis in vivo, by targeting BCL2 expression. MC2884-treatment reduced acetylation of the BCL2 promoter at higher level than combined p300 and EZH2 inhibition. This suggests a key role for BCL-2 reduction in potentiating responsiveness, also in combination therapy with BCL2 inhibitors. Finally, we identified both the mechanism of MC2884 action as well as a potential therapeutic scheme of its use. Altogether, this provides proof of concept for the use of epi-drugs coupled with epigenome analyses to 'personalize' precision medicine.
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40
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Zhou Y, Qiu YE, Qin SL, Luo Y, Cui R, Qin J, Chen JJ, Yu MH, Zhong M, Shi XY. Expression of CHD5 may serve as an independent biomarker of prognosis in colorectal cancer via immunohistochemical staining. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:2792-2798. [PMID: 31938397 PMCID: PMC6958296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 03/24/2018] [Indexed: 06/10/2023]
Abstract
Chromodomain helicase DNA binding protein 5 (CHD5) acts as a tumor suppressor in various types of cancer and belongs to CHD protein family. However, no prognostic role for CHD5 has yet been indicated in colorectal cancer. Therefore, the aim of this study was to investigate a possible association between CHD5 expression and colorectal cancer prognosis. Furthermore, immunochemistry was used to investigate CHD5 expression in 310 CRC tissue specimens. Expression of CHD5 significantly positively correlated with the lymphatic metastasis (P=0.007). The prognostic value of CHD5 in relation to overall survival was analyzed by Kaplan-Meier analysis and Cox proportional hazard models. The mean and medium follow-up times after surgery were 5.5 and 6.6 years, respectively. A total of 150 patients died during the 13 years of follow-up in the survey period. We also demonstrated that overall survival was poor in CRC patients with low expression of CHD5 (P=0.003). Accordingly, multivariate analysis identified low CHD5 expression as an independent risk factor (P=0.014), especially in elderly patients or those with late stage cancers. We suggest that CHD5 could serve as an independent prognostic biomarker for colorectal patients. This finding also should be verified by other research groups.
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Affiliation(s)
- Yong Zhou
- Department of Gastrointestinal Surgery, Jiading Hospital of Traditional Chinese Medicine222 Bole Road, Shanghai 201800, PR China
| | - Yi-Er Qiu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Shao-Lan Qin
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Yang Luo
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Ran Cui
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Jun Qin
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Jian-Jun Chen
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Min-Hao Yu
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Ming Zhong
- Department of Gastrointestinal Surgery, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong UniversityShanghai, PR China
| | - Xing-Yao Shi
- Department of Gastrointestinal Surgery, Jiading Hospital of Traditional Chinese Medicine222 Bole Road, Shanghai 201800, PR China
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41
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Guerra-Calderas L, González-Barrios R, Patiño CC, Alcaraz N, Salgado-Albarrán M, de León DC, Hernández CC, Sánchez-Pérez Y, Maldonado-Martínez HA, De la Rosa-Velazquez IA, Vargas-Romero F, Herrera LA, García-Carrancá A, Soto-Reyes E. CTCF-KDM4A complex correlates with histone modifications that negatively regulate CHD5 gene expression in cancer cell lines. Oncotarget 2018; 9:17028-17042. [PMID: 29682202 PMCID: PMC5908303 DOI: 10.18632/oncotarget.24798] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Accepted: 02/26/2018] [Indexed: 11/25/2022] Open
Abstract
Histone demethylase KDM4A is involved in H3K9me3 and H3K36me3 demethylation, which are epigenetic modifications associated with gene silencing and RNA Polymerase II elongation, respectively. KDM4A is abnormally expressed in cancer, affecting the expression of multiple targets, such as the CHD5 gene. This enzyme localizes at the first intron of CHD5, and the dissociation of KDM4A increases gene expression. In vitro assays showed that KDM4A-mediated demethylation is enhanced in the presence of CTCF, suggesting that CTCF could increase its enzymatic activity in vivo, however the specific mechanism by which CTCF and KDM4A might be involved in the CHD5 gene repression is poorly understood. Here, we show that CTCF and KDM4A form a protein complex, which is recruited into the first intron of CHD5. This is related to a decrease in H3K36me3/2 histone marks and is associated with its transcriptional downregulation. Depletion of CTCF or KDM4A by siRNA, triggered the reactivation of CHD5 expression, suggesting that both proteins are involved in the negative regulation of this gene. Furthermore, the knockout of KDM4A restored the CHD5 expression and H3K36me3 and H3K36me2 histone marks. Such mechanism acts independently of CHD5 promoter DNA methylation. Our findings support a novel mechanism of epigenetic repression at the gene body that does not involve promoter silencing.
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Affiliation(s)
- Lissania Guerra-Calderas
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Rodrigo González-Barrios
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Carlos César Patiño
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Nicolás Alcaraz
- The Bioinformatics Centre, Section for RNA and Computational Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Marisol Salgado-Albarrán
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - David Cantú de León
- Clinical Research, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | - Clementina Castro Hernández
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Yesennia Sánchez-Pérez
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
| | | | - Inti A De la Rosa-Velazquez
- Genomics Lab, Universidad Nacional Autónoma de México, Red de Apoyo a la Investigación-CIC and Instituto Nacional de Ciencias Médicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Fernanda Vargas-Romero
- Instituto de Fisiologia Celular-Neurociencias, Universidad Nacional Autonoma de Mexico (UNAM), Mexico City, Mexico
| | - Luis A Herrera
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Alejandro García-Carrancá
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico.,Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Ernesto Soto-Reyes
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología (INCan), Mexico City, Mexico
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42
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Costa RA, Seuánez HN. Investigation of major genetic alterations in neuroblastoma. Mol Biol Rep 2018; 45:287-295. [PMID: 29455316 DOI: 10.1007/s11033-018-4161-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 02/08/2018] [Indexed: 12/11/2022]
Abstract
Neuroblastoma (NB) is the most common extracranial solid tumor in childhood. This malignancy shows a wide spectrum of clinical outcome and its prognosis is conditioned by manifold biological and genetic factors. We investigated the tumor genetic profile and clinical data of 29 patients with NB by multiplex ligation-dependent probe amplification (MLPA) to assess therapeutic risk. In 18 of these tumors, MYCN status was assessed by fluorescence in situ hybridization (FISH). Copy number variation was also determined for confirming MLPA findings in two 6p loci. We found 2p, 7q and 17q gains, and 1p and 11q losses as the most frequent chromosome alterations in this cohort. FISH confirmed all cases of MYCN amplification detected by MLPA. In view of unexpected 6p imbalance, copy number variation of two 6p loci was assessed for validating MLPA findings. Based on clinical data and genetic profiles, patients were stratified in pretreatment risk groups according to international consensus. MLPA proved to be effective for detecting multiple genetic alterations in all chromosome regions as requested by the International Neuroblastoma Risk Group (INRG) for therapeutic stratification. Moreover, this technique proved to be cost effective, reliable, only requiring standard PCR equipment, and attractive for routine analysis. However, the observed 6p imbalances made PKHD1 and DCDC2 inadequate for control loci. This must be considered when designing commercial MLPA kits for NB. Finally, four patients showed a normal MLPA profile, suggesting that NB might have a more complex genetic pattern than the one assessed by presently available MLPA kits.
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Affiliation(s)
- Régis Afonso Costa
- Genetics Program, Instituto Nacional de Câncer, Rua André Cavalcanti 37, Rio de Janeiro, RJ, 20231-050, Brazil.,Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Héctor N Seuánez
- Genetics Program, Instituto Nacional de Câncer, Rua André Cavalcanti 37, Rio de Janeiro, RJ, 20231-050, Brazil. .,Department of Genetics, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
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43
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Durinck K, Speleman F. Epigenetic regulation of neuroblastoma development. Cell Tissue Res 2018; 372:309-324. [PMID: 29350283 DOI: 10.1007/s00441-017-2773-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/16/2017] [Indexed: 02/07/2023]
Abstract
In recent years, technological advances have enabled a detailed landscaping of the epigenome and the mechanisms of epigenetic regulation that drive normal cell function, development and cancer. Rather than merely a structural entity to support genome compaction, we now look at chromatin as a very dynamic and essential constellation that is actively participating in the tight orchestration of transcriptional regulation as well as DNA replication and repair. The unique feature of chromatin flexibility enabling fast switches towards more or less restricted epigenetic cellular states is, not surprisingly, intimately connected to cancer development and treatment resistance, and the central role of epigenetic alterations in cancer is illustrated by the finding that up to 50% of all mutations across cancer entities affect proteins controlling the chromatin status. We summarize recent insights into epigenetic rewiring underlying neuroblastoma (NB) tumor formation ranging from changes in DNA methylation patterns and mutations in epigenetic regulators to global effects on transcriptional regulatory circuits that involve key players in NB oncogenesis. Insights into the disruption of the homeostatic epigenetic balance contributing to developmental arrest of sympathetic progenitor cells and subsequent NB oncogenesis are rapidly growing and will be exploited towards the development of novel therapeutic strategies to increase current survival rates of patients with high-risk NB.
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Affiliation(s)
- Kaat Durinck
- Center for Medical Genetics, Ghent University, Ghent, Belgium.
| | - Frank Speleman
- Center for Medical Genetics, Ghent University, Ghent, Belgium
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Xu G, Zhu H, Zhang M, Xu J. Histone deacetylase 3 is associated with gastric cancer cell growth via the miR-454-mediated targeting of CHD5. Int J Mol Med 2018; 41:155-163. [PMID: 29115379 PMCID: PMC5746286 DOI: 10.3892/ijmm.2017.3225] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/07/2017] [Indexed: 12/20/2022] Open
Abstract
Gastric cancer (GC) is the third leading cause of cancer-related mortality in China and worlwide; hence, the identification of GC-related genes is necessary for the development of effective treatment strategies. In this study, histone deacetylase 3 (HDAC3) was identified as the most significantly upregulated cancer-related gene in GC tissues by microarray. In accordance with this, HDAC3 expression was found to be upregulated in GC cell lines/tissues. Further experiments indicated that the knockdown of HDAC3 decreased GC cell viability, reduced the colony formation number and decreased tumor weight. To explore the underlying mechanisms, the overexpression of HDAC3 was induced by transfection with an overexpression plasmid, followed by miRNA microarray, and we identified miR-454 as the most markedly upregulated miRNA. Accordingly, miR-454 expression was upregulated in GC cell lines/tissues and a high level of miR-454 indicated a high HDAC3 expression in GC tissues, and miR-454 knockdown reduced cell viability. In addition, a high level of miR-454 was significantly associated with an advanced clinical stage, lymph node metastases and a poor prognosis of patients with GC. Furthermore, CHD5 was identified as a direct target of miR-454. CHD5 was downregulated in GC tissues/cell lines and the expresssion of CHD5 inversely correlated with the level of miR-454 in GC tissues. Taken together, these observations indicate that HDAC3 is associated with GC cell growth via the miR-454-mediated targeting of CHD5.
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Affiliation(s)
| | | | - Minghui Zhang
- Department of Oncology, People's Hospital of Pudong, Shanghai 201299, P.R. China
| | - Jinhua Xu
- Department of Oncology, People's Hospital of Pudong, Shanghai 201299, P.R. China
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45
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Zhu X, Kong Q, Xie L, Chen Z, Li H, Zhu Z, Huang Y, Lan F, Luo H, Zhan J, Ding H, Lei J, Xiao Q, Fu W, Fan W, Zhang J, Luo H. The single-nucleotide polymorphisms in CHD5 affect the prognosis of patients with hepatocellular carcinoma. Oncotarget 2017; 9:13222-13230. [PMID: 29568352 PMCID: PMC5862573 DOI: 10.18632/oncotarget.23812] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2017] [Accepted: 11/19/2017] [Indexed: 12/20/2022] Open
Abstract
Previous studies showed that the low expressions of chromodomain-helicase-DNA-binding protein 5 (CHD5) were intensively associated with deteriorative biologic and clinical characteristics as well as outcomes in many tumors. The aim of this study is to determine whether CHD5 single nucleotide polymorphisms (SNPs) contribute to the prognosis of hepatocellular carcima (HCC). The SNPs were selected according to their linkage disequilibrium (LD) in the targeted next-generation sequencing (NGS) and then genotyped with TaqMan probers. We revealed a rare haplotype AG in CHD5 (SNPs: rs12564469-rs9434711) was markedly associated with HCC prognosis. The univariate and multivariate regression analyses revealed the patients with worse overall survival time were those with tumor metastasis and haplotype AG, as well as cirrhosis, poor differentiation and IV-TNM stage. Based on the available public databases, we discovered the significant association between haplotype AG and CHD5 mRNA expressions only existed in Chinese. These data proposed that the potentially genetic haplotype might functionally contribute to HCC prognosis and CHD5 mRNA expressions.
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Affiliation(s)
- Xiao Zhu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Cancer Center, Medical College of Georgia, Georgia Health Sciences University, Augusta, GA, USA.,Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | - Qingming Kong
- Immunity and Biochemical Research Lab, Zhejiang Academy of Medical Sciences, Hangzhou, China
| | - Liwei Xie
- Guangdong Institute of Microbiology, Guangzhou, China
| | - Zhihong Chen
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Hongmei Li
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Zhu Zhu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Yongmei Huang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
| | - Feifei Lan
- Forensic Identification Institute, Guangdong Women and Children Hospital, Guangzhou, China
| | - Haiqing Luo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,The Affiliated Hospital Cancer Center, Guangdong Medical University, Zhanjiang, China
| | - Jingting Zhan
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
| | - Hongrong Ding
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China
| | - Jinli Lei
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
| | - Qin Xiao
- Department of Blood Transfusion, Peking University Shenzhen Hospital, Shenzhen, China
| | - Weiming Fu
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, Guangdong, China
| | - Wenguo Fan
- Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University, Guangzhou, China
| | - Jinfang Zhang
- Key Laboratory of Orthopaedics and Traumatology, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, The First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Hui Luo
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, Dongguan Scientific Research Center, Guangdong Medical University, Dongguan, China.,Institute of Marine Medicine Research, Guangdong Medical University, Zhanjiang, China
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46
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Naraparaju K, Kolla V, Zhuang T, Higashi M, Iyer R, Kolla S, Okawa ER, Blobel GA, Brodeur GM. Role of microRNAs in epigenetic silencing of the CHD5 tumor suppressor gene in neuroblastomas. Oncotarget 2017; 7:15977-85. [PMID: 26895110 PMCID: PMC4941291 DOI: 10.18632/oncotarget.7434] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/05/2016] [Indexed: 02/07/2023] Open
Abstract
Neuroblastoma (NB), a tumor of the sympathetic nervous system, is the most common extracranial solid tumor of childhood. We and others have identified distinct patterns of genomic change that underlie diverse clinical behaviors, from spontaneous regression to relentless progression. We first identified CHD5 as a tumor suppressor gene that is frequently deleted in NBs. Mutation of the remaining CHD5 allele is rare in these tumors, yet expression is very low or absent, so expression is likely regulated by epigenetic mechanisms. In order to understand the potential role of miRNA regulation of CHD5 protein expression in NBs, we examined all miRNAs that are predicted to target the 3′-UTR using miRanda, TargetScan and other algorithms. We identified 18 miRNAs that were predicted by 2 or more programs: miR-204, -211, -216b, -17, -19ab, -20ab, -93, -106ab, -130ab, -301ab, -454, -519d, -3666. We then performed transient transfections in two NB cell lines, NLF (MYCN amplified) and SY5Y (MYCN non-amplified), with the reporter plasmid and miRNA mimic, as well as appropriate controls. We found seven miRNAs that significantly downregulated CHD5 expression in NB: miR-211, 17, -93, -20b, -106b, -204, and -3666. Interestingly, MYCN upregulates several of the candidates we identified: miR-17, -93, -106b & -20b. This suggests that miRNAs driven by MYCN and other genes represent a potential epigenetic mechanism to regulate CHD5 expression.
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Affiliation(s)
- Koumudi Naraparaju
- Division of Oncology and Hematology, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Venkatadri Kolla
- Division of Oncology and Hematology, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Tiangang Zhuang
- Division of Oncology and Hematology, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Mayumi Higashi
- Division of Oncology and Hematology, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Radhika Iyer
- Division of Oncology and Hematology, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Sriharsha Kolla
- Division of Oncology and Hematology, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Erin R Okawa
- Division of Oncology and Hematology, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Gerd A Blobel
- Department of Pediatrics, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
| | - Garrett M Brodeur
- Division of Oncology and Hematology, The Children's Hospital of Philadelphia, University of Pennsylvania, Philadelphia, PA, USA
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47
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A systems medicine approach for finding target proteins affecting treatment outcomes in patients with non-Hodgkin lymphoma. PLoS One 2017; 12:e0183969. [PMID: 28892521 PMCID: PMC5593188 DOI: 10.1371/journal.pone.0183969] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 08/15/2017] [Indexed: 02/07/2023] Open
Abstract
Autoantibody profiling with a systems medicine approach can help identify critical dysregulated signaling pathways (SPs) in cancers. In this way, immunoglobulins G (IgG) purified from the serum samples of 92 healthy controls, 10 pre-treated (PR) non-Hodgkin lymphoma (NHL) patients, and 20 NHL patients who underwent chemotherapy (PS) were screened with a phage-displayed random peptide library. Protein-protein interaction networks of the PR and PS groups were analyzed and visualized by Gephi. The results indicated AXIN2, SENP2, TOP2A, FZD6, NLK, HDAC2, HDAC1, and EHMT2, in addition to CAMK2A, PLCG1, PLCG2, GRM5, GRIN2B, GRIN2D, CACNA2D3, and SPTAN1 as hubs in 11 and 7 modules of PR and PS networks, respectively. PR- and PS-specific hubs were evaluated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Reactome databases. The PR-specific hubs were involved in Wnt SP, signaling by Notch1 in cancer, telomere maintenance, and transcriptional misregulation. In contrast, glutamate receptor SP, Fc receptor-related pathways, growth factors-related SPs, and Wnt SP were statistically significant enriched pathways, based on the pathway analysis of PS hubs. The results revealed that the most PR-specific proteins were associated with events involved in tumor development, while chemotherapy in the PS group was associated with side effects of drugs and/or cancer recurrence. As the findings demonstrated, PR- and PS-specific proteins in this study can be promising therapeutic targets in future studies.
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48
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Pisansky MT, Young AE, O'Connor MB, Gottesman II, Bagchi A, Gewirtz JC. Mice lacking the chromodomain helicase DNA-binding 5 chromatin remodeler display autism-like characteristics. Transl Psychiatry 2017; 7:e1152. [PMID: 28608855 PMCID: PMC5537637 DOI: 10.1038/tp.2017.111] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 04/20/2017] [Indexed: 12/12/2022] Open
Abstract
Although autism spectrum disorders (ASDs) share a core set of nosological features, they exhibit substantial genetic heterogeneity. A parsimonious hypothesis posits that dysregulated epigenetic mechanisms represent common pathways in the etiology of ASDs. To investigate this hypothesis, we generated a novel mouse model resulting from brain-specific deletion of chromodomain helicase DNA-binding 5 (Chd5), a chromatin remodeling protein known to regulate neuronal differentiation and a member of a gene family strongly implicated in ASDs. RNA sequencing of Chd5-/- mouse forebrain tissue revealed a preponderance of changes in expression of genes important in cellular development and signaling, sociocommunicative behavior and ASDs. Pyramidal neurons cultured from Chd5-/- cortex displayed alterations in dendritic morphology. Paralleling ASD nosology, Chd5-/- mice exhibited abnormal sociocommunicative behavior and a strong preference for familiarity. Chd5-/- mice further showed deficits in responding to the distress of a conspecific, a mouse homolog of empathy. Thus, dysregulated chromatin remodeling produces a pattern of transcriptional, neuronal and behavioral effects consistent with the presentation of ASDs.
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Affiliation(s)
- M T Pisansky
- Graduate Program in Neuroscience University of Minnesota —Twin Cities, Minneapolis, MN, USA
| | - A E Young
- Department of Psychology, University of Minnesota —Twin Cities, Minneapolis, MN, USA
| | - M B O'Connor
- Department of Genetics, Cell Biology, and Development, University of Minnesota —Twin Cities, Minneapolis, MN, USA
| | - I I Gottesman
- Department of Psychology, University of Minnesota —Twin Cities, Minneapolis, MN, USA
| | - A Bagchi
- Department of Genetics, Cell Biology, and Development, University of Minnesota —Twin Cities, Minneapolis, MN, USA
| | - J C Gewirtz
- Department of Psychology, University of Minnesota —Twin Cities, Minneapolis, MN, USA
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49
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Ni S, Ye M, Huang T. Short stature homeobox 2 methylation as a potential noninvasive biomarker in bronchial aspirates for lung cancer diagnosis. Oncotarget 2017; 8:61253-61263. [PMID: 28977861 PMCID: PMC5617421 DOI: 10.18632/oncotarget.18056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/25/2017] [Indexed: 12/16/2022] Open
Abstract
Gene methylation has been frequently observed in lung cancer. However, the use of methylated genes in bronchial aspirates of patients with lung cancer remains to be evaluated. The purpose of this study was to analyze whether the detection of genes with aberrant promoter methylation can be useful noninvasive biomarkers in bronchial aspirates from lung cancer. We found that the methylation status of the cyclin-dependent kinase inhibitor 2A (P16), Ras association domain family 1 isoform (RASSF1A), adenomatous polyposis coli (APC) and short stature homeobox 2 (SHOX2) genes was significantly correlated with lung cancer in bronchial aspirates. The P16, RASSF1A and APC methylation had a bad diagnostic effect in bronchial aspirates of patients with lung cancer compared with non-tumor controls (P16: sensitivity = 0.26, specificity = 0.99, area under the curve (AUC) = 0.67; RASSF1A: sensitivity = 0.40, specificity = 0.99, AUC = 0.66; APC: sensitivity = 0.17, specificity = 0.98, AUC = 0.65). The pooled sensitivity, specificity, and AUC of the SHOX2 methylation were 0.75, 0.94, and 0.94, respectively. Moreover, when squamous cell carcinoma (SCC) was compared to adenocarcinoma (AC), the SHOX2 gene had a significantly higher methylation rate in SCC than in AC (P < 0.001). Methylated P16, RASSF1A, APC and retinoic acid receptor beta2 (RARβ2) genes had similar frequencies in these two histotypes (P > 0.1). Our findings suggest that methylated SHOX2 gene could be a specific and potential noninvasive biomarker using bronchial aspirates for lung cancer diagnosis, especially for SCC.
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Affiliation(s)
- Shumin Ni
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, People's Republic of China
| | - Meng Ye
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, People's Republic of China
| | - Tao Huang
- The Affiliated Hospital of Ningbo University, Ningbo, Zhejiang 315020, People's Republic of China
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50
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Baykara O, Tansarikaya M, Bulut P, Demirkaya A, Buyru N. CHD5 is a potential tumor suppressor in non small cell lung cancer (NSCLC). Gene 2017; 618:65-68. [PMID: 28400267 DOI: 10.1016/j.gene.2017.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 03/17/2017] [Accepted: 04/07/2017] [Indexed: 01/17/2023]
Abstract
Lung cancer is one of the deadliest types of cancers and genetic and epigenetic alterations play major roles in its development. Chromodomain (CHD) protein family acts in chromatin organization, regulation of transcription and also genomic stability and cancer prevention. Although CHD5, a member of this family was shown to contribute to major cellular events and functions as a tumor suppressor gene in various types of cancer, it is not clear whether CHD5 plays a role in lung carcinogenesis. The aim of this study was to investigate the possible role of CHD5 in progression of non-small cell lung cancer (NSCLC). Expression levels of CHD5 gene in 59 tumor and corresponding non-cancerous lung tissue samples were analyzed by qRT-PCR and the methylation status of the promoter region was investigated by methylation specific PCR (MS-PCR). The Akt phosphorylation levels were investigated by Western Blot (WB). CHD5 was down-regulated in 17 (39.5%) and up-regulated in 24 (55.8%) of tumor specimens. Even though the promoter of CHD5 was hypermethylated in 8 patients, it was not found associated with CHD5 gene expression (p=0.08). Akt phosphorylation was increased in 14 (53.8%) and decreased in 12 (46.2%) of the samples but no significant association was found between p-Akt phosphorylation and CHD5 expression (p=0.67). We suggest that CHD5 may act as a tumor suppressor gene in NSCLC.
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Affiliation(s)
- Onur Baykara
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey
| | - Merve Tansarikaya
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey
| | - Pelin Bulut
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey
| | - Ahmet Demirkaya
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Thoracic Surgery, Istanbul 34098, Turkey
| | - Nur Buyru
- Istanbul University Cerrahpasa Medical Faculty, Dept. of Medical Biology and Genetics, Istanbul 34098, Turkey.
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