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Stuckel AJ, Zeng S, Lyu Z, Zhang W, Zhang X, Dougherty U, Mustafi R, Khare T, Zhang Q, Joshi T, Bissonnette M, Khare S. Sprouty4 is epigenetically upregulated in human colorectal cancer. Epigenetics 2023; 18:2145068. [PMID: 36384366 PMCID: PMC9980603 DOI: 10.1080/15592294.2022.2145068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sprouty4 (SPRY4) has been frequently reported as a tumor suppressor and is therefore downregulated in various cancers. For the first time, we report that SPRY4 is epigenetically upregulated in colorectal cancer (CRC). In this study, we explored DNA methylation and hydroxymethylation levels of SPRY4 in CRC cells and patient samples and correlated these findings with mRNA and protein expression levels. Three loci within the promoter region of SPRY4 were evaluated for 5mC levels in CRC using the combined bisulfite restriction analysis. In addition, hydroxymethylation levels within SPRY4 were measured in CRC patients. Lastly, DNA methylation and mRNA expression data were extracted from CRC patients in multiple high-throughput data repositories like Gene Expression Omnibus and The Cancer Genome Atlas. Combined in vitro and in silico analysis of promoter methylation levels of SPRY4 clearly demonstrates that the distal promoter region undergoes hypomethylation in CRC patients and is associated with increased expression. Moreover, a decrease in gene body hydroxymethylation and an increase in gene body methylation within the coding region of SPRY4 were found in CRC patients and correlated with increased expression. SPRY4 is epigenetically upregulated in CRC by promoter hypomethylation and hypermethylation within the gene body that warrants future investigation of atypical roles of this established tumor suppressor.
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Affiliation(s)
- Alexei J. Stuckel
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA
| | - Shuai Zeng
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65201, USA,Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, 65201, USA
| | - Zhen Lyu
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65201, USA,Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, 65201, USA
| | - Wei Zhang
- Department of Preventive Medicine and the Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, 60611, USA
| | - Xu Zhang
- Department of Medicine, University of Illinois, Chicago, Illinois, 60607, USA
| | - Urszula Dougherty
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition; the University of Chicago, Chicago, Illinois, 60637, USA
| | - Reba Mustafi
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition; the University of Chicago, Chicago, Illinois, 60637, USA
| | - Tripti Khare
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA
| | - Qiong Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA
| | - Trupti Joshi
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, 65201, USA,Institute for Data Science and Informatics, University of Missouri, Columbia, Missouri, 65211, USA,Department of Health Management and Informatics; School of Medicine, University of Missouri, Columbia, Missouri, 65212, USA
| | - Marc Bissonnette
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition; the University of Chicago, Chicago, Illinois, 60637, USA
| | - Sharad Khare
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA,Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri, 65201, USA,CONTACT Sharad Khare Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri, 65212, USA
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Stuckel AJ, Khare T, Bissonnette M, Khare S. Aberrant regulation of CXCR4 in cancer via deviant microRNA-targeted interactions. Epigenetics 2022; 17:2318-2331. [PMID: 36047714 PMCID: PMC9665135 DOI: 10.1080/15592294.2022.2118947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 08/02/2022] [Accepted: 08/18/2022] [Indexed: 11/03/2022] Open
Abstract
CXCR4 is involved in many facets of cancer, including being a major player in establishing metastasis. This is in part due to the deregulation of CXCR4, which can be attributed to many genetic and epigenetic mechanisms, including aberrant microRNA-CXCR4 interaction. MicroRNAs (miRNAs) are a type of small non-coding RNA that primarily targets the 3' UTR of mRNA transcripts, which in turn suppresses mRNA and subsequent protein expression. In this review, we reported and characterized the many aberrant miRNA-CXCR4 interactions that occur throughout human cancers. In particular, we reported known target sequences located on the 3' UTR of CXCR4 transcripts that tumour suppressor miRNAs bind and therefore regulate expression by. From these aberrant interactions, we also documented affected downstream genes/pathways and whether a particular tumour suppressor miRNA was reported as a prognostic marker in its respected cancer type. In addition, a limited number of cancer-causing miRNAs coined 'oncomirs' were reported and described in relation to CXCR4 regulation. Moreover, the mechanisms underlying both tumour suppressor and oncomir deregulations concerning CXCR4 expression were also explored. Furthermore, the miR-146a-CXCR4 axis was delineated in oncoviral infected endothelial cells in the context of virus-causing cancers. Lastly, miRNA-driven therapies and CXCR4 antagonist drugs were discussed as potential future treatment options in reported cancers pertaining to deregulated miRNA-CXCR4 interactions.
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Affiliation(s)
- Alexei J. Stuckel
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri65212, USA
| | - Tripti Khare
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri65212, USA
| | - Marc Bissonnette
- Section of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Chicago, Chicago, Il60637, USA
| | - Sharad Khare
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, Missouri65212, USA
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, Missouri65201, USA
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Stuckel AJ, Zhang W, Zhang X, Zeng S, Dougherty U, Mustafi R, Zhang Q, Perreand E, Khare T, Joshi T, West-Szymanski DC, Bissonnette M, Khare S. Correction: Stuckel, et al.; Enhanced CXCR4 Expression Associates with Increased Gene Body 5-Hydroxymethylcytosine Modification but Not Decreased Promoter Methylation in Colorectal Cancer. Cancers 2020, 12, 539. Cancers (Basel) 2020; 12:cancers12113104. [PMID: 33114273 PMCID: PMC7690871 DOI: 10.3390/cancers12113104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/15/2020] [Indexed: 11/21/2022] Open
Affiliation(s)
- Alexei J. Stuckel
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, MO 65212, USA; (A.J.S.); (Q.Z.); (E.P.); (T.K.)
| | - Wei Zhang
- Department of Preventive Medicine and The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA;
| | - Xu Zhang
- Department of Medicine, University of Illinois, Chicago, IL 60607, USA;
| | - Shuai Zeng
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65201, USA; (S.Z.); (T.J.)
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65201, USA
| | - Urszula Dougherty
- Section of Gastroenterology, Hepatology and Nutrition, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA; (U.D.); (R.M.); (D.C.W.-S.); (M.B.)
| | - Reba Mustafi
- Section of Gastroenterology, Hepatology and Nutrition, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA; (U.D.); (R.M.); (D.C.W.-S.); (M.B.)
| | - Qiong Zhang
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, MO 65212, USA; (A.J.S.); (Q.Z.); (E.P.); (T.K.)
| | - Elsa Perreand
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, MO 65212, USA; (A.J.S.); (Q.Z.); (E.P.); (T.K.)
| | - Tripti Khare
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, MO 65212, USA; (A.J.S.); (Q.Z.); (E.P.); (T.K.)
| | - Trupti Joshi
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65201, USA; (S.Z.); (T.J.)
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Diana C. West-Szymanski
- Section of Gastroenterology, Hepatology and Nutrition, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA; (U.D.); (R.M.); (D.C.W.-S.); (M.B.)
| | - Marc Bissonnette
- Section of Gastroenterology, Hepatology and Nutrition, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA; (U.D.); (R.M.); (D.C.W.-S.); (M.B.)
| | - Sharad Khare
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Missouri, Columbia, MO 65212, USA; (A.J.S.); (Q.Z.); (E.P.); (T.K.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Correspondence: or
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Kumar SR, Kimchi ET, Manjunath Y, Gajagowni S, Stuckel AJ, Kaifi JT. Author Correction: RNA cargos in extracellular vesicles derived from blood serum in pancreas associated conditions. Sci Rep 2020; 10:9981. [PMID: 32546785 PMCID: PMC7298053 DOI: 10.1038/s41598-020-66766-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Senthil R Kumar
- Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA. .,Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, 65212, USA. .,Harry S. Truman Veterans Hospital, 800 Hospital Drive, Columbia, MO, 65212, USA.
| | - Eric T Kimchi
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.,Harry S. Truman Veterans Hospital, 800 Hospital Drive, Columbia, MO, 65212, USA
| | - Yariswamy Manjunath
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.,Harry S. Truman Veterans Hospital, 800 Hospital Drive, Columbia, MO, 65212, USA
| | - Saivaroon Gajagowni
- Veterinary Medicine & Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Alexei J Stuckel
- Harry S. Truman Veterans Hospital, 800 Hospital Drive, Columbia, MO, 65212, USA.,Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, MO, 65212, USA
| | - Jussuf T Kaifi
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO, 65212, USA.,Harry S. Truman Veterans Hospital, 800 Hospital Drive, Columbia, MO, 65212, USA
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Stuckel AJ, Zhang W, Zhang X, Zeng S, Dougherty U, Mustafi R, Zhang Q, Perreand E, Khare T, Joshi T, West-Szymanski DC, Bissonnette M, Khare S. Enhanced CXCR4 Expression Associates with Increased Gene Body 5-Hydroxymethylcytosine Modification but not Decreased Promoter Methylation in Colorectal Cancer. Cancers (Basel) 2020; 12:cancers12030539. [PMID: 32110952 PMCID: PMC7139960 DOI: 10.3390/cancers12030539] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/19/2020] [Accepted: 02/24/2020] [Indexed: 12/19/2022] Open
Abstract
In colorectal cancer (CRC), upregulation of the C-X-C motif chemokine receptor 4 (CXCR4) is correlated with metastasis and poor prognosis, highlighting the need to further elucidate CXCR4’s regulation in CRC. For the first time, DNA methylation and 5-hydroxymethylcytosine aberrations were investigated to better understand the epigenetic regulation of CXCR4 in CRC. CXCR4 expression levels were measured using qPCR and immunoblotting in normal colon tissues, primary colon cancer tissues and CRC cell lines. Publicly available RNA-seq and methylation data from The Cancer Genome Atlas (TCGA) were extracted from tumors from CRC patients. The DNA methylation status spanning CXCR4 gene was evaluated using combined bisulfite restriction analysis (COBRA). The methylation status in the CXCR4 gene body was analyzed using previously performed nano-hmC-seal data from colon cancers and adjacent normal colonic mucosa. CXCR4 expression levels were significantly increased in tumor stromal cells and in tumor colonocytes, compared to matched cell types from adjacent normal-appearing mucosa. CXCR4 promoter methylation was detected in a minority of colorectal tumors in the TCGA. The CpG island of the CXCR4 promoter showed increased methylation in three of four CRC cell lines. CXCR4 protein expression differences were also notable between microsatellite stable (MSS) and microsatellite instable (MSI) tumor cell lines. While differential methylation was not detected in CXCR4, enrichment of 5-hydroxymethylcytosine (5hmC) in CXCR4 gene bodies in CRC was observed compared to adjacent mucosa.
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Affiliation(s)
- Alexei J. Stuckel
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, MO 65212, USA (Q.Z.); (E.P.); (T.K.)
| | - Wei Zhang
- Department of Preventive Medicine and The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA;
| | - Xu Zhang
- Department of Medicine, University of Illinois, Chicago, IL 60607, USA;
| | - Shuai Zeng
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65201, USA; (S.Z.); (T.J.)
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65201, USA
| | - Urszula Dougherty
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition, The University of Chicago, Chicago, IL 60637, USA; (U.D.); (R.M.); (D.C.W.-S.); (M.B.)
| | - Reba Mustafi
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition, The University of Chicago, Chicago, IL 60637, USA; (U.D.); (R.M.); (D.C.W.-S.); (M.B.)
| | - Qiong Zhang
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, MO 65212, USA (Q.Z.); (E.P.); (T.K.)
| | - Elsa Perreand
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, MO 65212, USA (Q.Z.); (E.P.); (T.K.)
| | - Tripti Khare
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, MO 65212, USA (Q.Z.); (E.P.); (T.K.)
| | - Trupti Joshi
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65201, USA; (S.Z.); (T.J.)
- Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Department of Health Management and Informatics, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Diana C. West-Szymanski
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition, The University of Chicago, Chicago, IL 60637, USA; (U.D.); (R.M.); (D.C.W.-S.); (M.B.)
| | - Marc Bissonnette
- Department of Medicine, Section of Gastroenterology, Hepatology and Nutrition, The University of Chicago, Chicago, IL 60637, USA; (U.D.); (R.M.); (D.C.W.-S.); (M.B.)
| | - Sharad Khare
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Missouri, Columbia, MO 65212, USA (Q.Z.); (E.P.); (T.K.)
- Harry S. Truman Memorial Veterans’ Hospital, Columbia, MO 65201, USA
- Correspondence:
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Almamun M, Kholod O, Stuckel AJ, Levinson BT, Johnson NT, Arthur GL, Davis JW, Taylor KH. Inferring a role for methylation of intergenic DNA in the regulation of genes aberrantly expressed in precursor B-cell acute lymphoblastic leukemia. Leuk Lymphoma 2017; 58:1-12. [PMID: 28094574 DOI: 10.1080/10428194.2016.1272683] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A complete understanding of the mechanisms involved in the development of pre-B ALL is lacking. In this study, we integrated DNA methylation data and gene expression data to elucidate the impact of aberrant intergenic DNA methylation on gene expression in pre-B ALL. We found a subset of differentially methylated intergenic loci that were associated with altered gene expression in pre-B ALL patients. Notably, 84% of these regions were also bound by transcription factors (TF) known to play roles in differentiation and B-cell development in a lymphoblastoid cell line. Further, an overall downregulation of eRNA transcripts was observed in pre-B ALL patients and these transcripts were associated with the downregulation of putative target genes involved in B-cell migration, proliferation, and apoptosis. The identification of novel putative regulatory regions highlights the significance of intergenic DNA sequences and may contribute to the identification of new therapeutic targets for the treatment of pre-B ALL.
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Affiliation(s)
- Md Almamun
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Olha Kholod
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Alexei J Stuckel
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Benjamin T Levinson
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - Nathan T Johnson
- b Bioinformatics and Computational Biology , Worcester Polytechnic Institute , Worcester , MA , USA
| | - Gerald L Arthur
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
| | - J Wade Davis
- c Department of Health Management and Informatics , University of Missouri-Columbia , Columbia , MO , USA
| | - Kristen H Taylor
- a Department of Pathology and Anatomical Sciences , University of Missouri-Columbia , Columbia , MO , USA
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