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Almutairi MH, Alrubie TM, Alshareeda AT, Albarakati N, Almotiri A, Alamri AM, Almutairi BO, Alanazi M. Differential expression and regulation of ADAD1, DMRTC2, PRSS54, SYCE1, SYCP1, TEX101, TEX48, and TMPRSS12 gene profiles in colon cancer tissues and their in vitro response to epigenetic drugs. PLoS One 2024; 19:e0307724. [PMID: 39208330 PMCID: PMC11361649 DOI: 10.1371/journal.pone.0307724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 07/10/2024] [Indexed: 09/04/2024] Open
Abstract
Colon cancer (CC) is a significant cause of death worldwide, particularly in Saudi Arabia. To increase the accuracy of diagnosis and treatment, it is important to discover new specific biomarkers for CC. The main objectives of this research are to identify potential specific biomarkers for the early diagnosis of CC by analyzing the expressions of eight cancer testis (CT) genes, as well as to analyze how epigenetic mechanisms control the expression of these genes in CC cell lines. Tissue samples were collected from 15 male patients with CC tissues and matched NC tissues for gene expression analysis. The expression levels of specific CT genes, including ADAD1, DMRTC2, PRSS54, SYCE1, SYCP1, TEX101, TEX48, and TMPRSS12, were assessed using quantitative techniques. To validate the gene expression patterns, we used publicly available CC statistics. To investigate the effect of inhibition of DNA methylation and histone deacetylation on CT gene expression, in vitro experiments were performed using HCT116 and Caco-2 cell lines. There was no detected expression of the genes neither in the patient samples nor in NC tissues, except for TEX48, which exhibited upregulation in CC samples compared to NC tissues in online datasets. Notably, CT genes showed expression in testis samples. In vitro, experiments demonstrated significant enhancement in mRNA expression levels of ADAD1, DMRTC2, PRSS54, SYCE1, SYCP1, TEX101, TEX48, and TMPRSS12 following treatment with 5-aza-2'-deoxycytidine and trichostatin A in HCT116 and Caco-2 cell lines. Epigenetic treatments modify the expression of CT genes, indicating that these genes can potentially be used as biomarkers for CC. The importance of conducting further research to understand and target epigenetic mechanisms to improve CC treatment cannot be overemphasized.
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Affiliation(s)
- Mikhlid H. Almutairi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Turki M. Alrubie
- Laboratories Directorate, General Directorate of Animal Health, Ministry Deputyship for Agriculture, Ministry of Environment, Water and Agriculture, Riyadh, Saudi Arabia
| | - Alaa T. Alshareeda
- Blood and Cancer Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Nada Albarakati
- Blood and Cancer Research Department, King Abdullah International Medical Research Center, King Saud bin Abdulaziz University for Health Sciences, Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia
| | - Alhomidi Almotiri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Ad Dawadmi, Saudi Arabia
| | - Abdullah M. Alamri
- Department of Biochemistry, Genome Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Bader O. Almutairi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Alanazi
- Department of Biochemistry, Genome Research Chair, College of Science, King Saud University, Riyadh, Saudi Arabia
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Almatrafi AM, Alamery S, Almutairi MH. Expression pattern analysis of the MAGE family genes in breast cancer patients and hypomethylation activation in the MCF-7 cells. Heliyon 2024; 10:e34506. [PMID: 39082035 PMCID: PMC11284374 DOI: 10.1016/j.heliyon.2024.e34506] [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: 09/20/2023] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 08/02/2024] Open
Abstract
Melanoma antigen gene (MAGE) families are cancer-testis genes that normally show expression in the testes. However, their expressions have been linked with various types of human cancers, including BC. Therefore, the primary purposes of the present research were to assess the expression of MAGE-A, -B, and -C genes in Saudi female patients with BC and determine their regulation via the epigenetic mechanism. Ten BC samples were analyzed for the expression levels of nine MAGE-A genes, six MAGE-B genes, and three MAGE-C genes using the RT-PCR technique. All 18 evaluated genes except for MAGE-A1, -A3, -A4, and -B5 showed weak band expressions in some BC specimens. MAGE-A6 and -B2 were expressed in 40 % of the BC tissue samples, and MAGE-A9, -A10, and -B6 were expressed in 30 %. The lowest expression levels were found for MAGE-A11, -B1, -B3, -B4, -C1, and -C2 in 10 % of the BC specimens and for MAGE-A9,--B2, and --C3 in 20 % of the samples. The most frequently expressed gene was MAGE-A8 (found in 70 % of the BC samples), which suggests that it may serve as - a marker for screening of BC. In vitro treatment, the 5-aza-2'-deoxycytidine agent led to a significant rise in mRNA expressions for all tested genes related to the MAGE-A family, except for MAGE-A10. By contrast, among the genes in the MAGE-B and -C families, only MAGE-B1 and -C2 exhibited detectable mRNA expression levels after treatment.
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Affiliation(s)
- Ahmad M. Almatrafi
- Department of Biology, College of Science, Taibah University, Medina, Saudi Arabia
| | - Salman Alamery
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
| | - Mikhlid H. Almutairi
- Zoology Department, College of Science, King Saud University, P.O. Box 2455, Riyadh, 11451, Saudi Arabia
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Alrubie TM, Shaik JP, Alamri AM, Alanazi M, Alshareeda AT, alqarni A, Alawfi HG, Almaiman SM, Almutairi MH. FTHL17, PRM2, CABYR, CPXCR1, ADAM29, and CABS1 are highly expressed in colon cancer patients and are regulated in vitro by epigenetic alterations. Heliyon 2024; 10:e23689. [PMID: 38187237 PMCID: PMC10767510 DOI: 10.1016/j.heliyon.2023.e23689] [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: 06/29/2023] [Revised: 11/29/2023] [Accepted: 12/09/2023] [Indexed: 01/09/2024] Open
Abstract
Background Colon cancer is a serious public health issue and a major cause of cancer-related mortality worldwide, including Saudi Arabia. Knowledge of genes associated with colon cancer development and progression is essential for identifying new cancer-specific biomarkers to improve the diagnosis of colon cancer. Methods The expression levels of FTHL17, PRM2, CABYR, CPXCR1, ADAM29, and CABS1 in 15 adjacent colon cancer and normal colon tissue samples from male patients were investigated using reverse transcription polymerase chain reaction (RT-PCR) and quantitative RT-PCR (qRT-PCR) assays. qRT-PCR analysis was also used to determine whether reducing DNA methyltransferase (via 5-aza-2'-deoxycytidine treatment) or histone deacetylation (via trichostatin treatment) increased the expression levels of the tested genes. Results The analysis of the 15 colon cancer and adjacent normal colon tissue samples revealed that all six genes were expressed in both groups, but their expression levels were significantly higher in the colon cancer group. Furthermore, the mRNA expression levels of the FTHL17, PRM2, CABYR, CPXCR1, and ADAM29 genes were considerably upregulated after treatment of HCT116 and Caco-2 cells with 5-aza-2'-deoxycytidine and trichostatin. However, the CABS1 gene was activated only with trichostatin treatment. Conclusions The findings of this study suggest that FTHL17, PRM2, CABYR, CPXCR1, ADAM29, and CABS1 are suitable candidate biomarkers of colon cancer and their expressions are regulated by hypomethylation and hyperacetylation.
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Affiliation(s)
- Turki M. Alrubie
- Zoology Department, College of Science, King Saud University, P.O. Box: 2455, 11451, Riyadh, Saudi Arabia
| | - Jilani P. Shaik
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah M. Alamri
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad Alanazi
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Alaa T. Alshareeda
- Blood and Cancer Research Department, King Abdullah International Medical Research Center, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Ayyob alqarni
- Department of Surgery, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Homoud G. Alawfi
- Department of Surgery, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Sarah M. Almaiman
- Department of Anatomic Pathology, King Abdulaziz Medical City, Ministry of National Guard Health Affairs, Riyadh, Saudi Arabia
| | - Mikhlid H. Almutairi
- Zoology Department, College of Science, King Saud University, P.O. Box: 2455, 11451, Riyadh, Saudi Arabia
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Alrubie TM, Alamri AM, Almutairi BO, Alrefaei AF, Arafah MM, Alanazi M, Semlali A, Almutairi MH. Higher Expression Levels of SSX1 and SSX2 in Patients with Colon Cancer: Regulated In Vitro by the Inhibition of Methylation and Histone Deacetylation. MEDICINA (KAUNAS, LITHUANIA) 2023; 59:medicina59050988. [PMID: 37241221 DOI: 10.3390/medicina59050988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 05/13/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
Background and Objectives: Colon cancer (CC) has a high mortality rate and is often diagnosed at an advanced stage in Saudi Arabia. Thus, the identification and characterization of potential new cancer-specific biomarkers are imperative for improving the diagnosis of CC by detecting it at an early stage. Cancer-testis (CT) genes have been identified as potential biomarkers for the early diagnosis of various cancers. Among the CT genes are those belonging to the SSX family. In order to assess the usefulness of SSX family genes as cancer biomarkers for the detection of early-stage CC, the goal of this research was to validate the expressions of these genes in patients with CC and in matched patients with normal colons (NCs). Materials and Methods: RT-PCR assays were used to analyze the SSX1, SSX2, and SSX3 family gene expression levels in 30 neighboring NC and CC tissue samples from male Saudi patients. Epigenetic alterations were also tested in vitro using qRT-PCR analysis to determine whether reduced DNA methyltransferase or histone deacetylation could stimulate SSX gene expression via 5-aza-2'-deoxycytidine and trichostatin treatments, respectively. Results: The RT-PCR results showed SSX1 and SSX2 gene expression in 10% and 20% of the CC tissue specimens, respectively, but not in any of the NC tissue specimens. However, no SSX3 expression was detected in any of the examined CC or NC tissue samples. In addition, the qRT-PCR results showed significantly higher SSX1 and SSX2 expression levels in the CC tissue samples than in the NC tissue samples. The 5-aza-2'-deoxycytidine and trichostatin treatments significantly induced the mRNA expression levels of the SSX1, SSX2, and SSX3 genes in the CC cells in vitro. Conclusions: These findings suggest that SSX1 and SSX2 are potentially suitable candidate biomarkers for CC. Their expressions can be regulated via hypomethylating and histone deacetylase treatments, subsequently providing a potential therapeutic target for CC.
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Affiliation(s)
- Turki M Alrubie
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah M Alamri
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
| | - Bader O Almutairi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdulwahed F Alrefaei
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Maha M Arafah
- Pathology Department, College of Medicine, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Alanazi
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11495, Saudi Arabia
| | - Abdelhabib Semlali
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, 2420 Rue de la Terrasse, Local 1758, Québec, QC G1V 0A6, Canada
| | - Mikhlid H Almutairi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Almutairi MH, Alrubie TM, Almutairi BO, Alamri AM, Alrefaei AF, Arafah MM, Alanazi M, Semlali A. The Expression Patterns of Human Cancer-Testis Genes Are Induced through Epigenetic Drugs in Colon Cancer Cells. Pharmaceuticals (Basel) 2022; 15:1319. [PMID: 36355490 PMCID: PMC9692864 DOI: 10.3390/ph15111319] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/28/2022] [Accepted: 10/21/2022] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND The expression of human germline genes is restricted to the germ cells of the gonads, which produce sperm and eggs. The germline genes involved in testis development and potentially activated in cancer cells are known as cancer-testis (CT) genes. These genes are potential therapeutic targets and biomarkers, as well as drivers of the oncogenic process. CT genes can be reactivated by treatment with drugs that demethylate DNA. The majority of the existing literature on CT gene activation focuses on X-chromosome-produced CT genes. We tested the hypothesis that epigenetic landscape changes, such as DNA methylation, can alter several CT gene expression profiles in cancer and germ cells. METHODS Colon cancer (CC) cell lines were treated with the DNA methyltransferase inhibitor (DNMTi) 5-aza-2'-deoxycytidine, or with the histone deacetylase inhibitor (HDACi) trichostatin A (TSA). The effects of these epigenetic treatments on the transcriptional activation of previously published CT genes (CTAG1A, SCP2D1, TKTL2, LYZL6, TEX33, and ACTRT1) and testis-specific genes (NUTM1, ASB17, ZSWIM2, ADAM2, and C10orf82) were investigated. RESULTS We found that treatment of CC cell lines with 5-aza-2'-deoxycytidine or TSA correlated with activation of X-encoded CT genes and non-X-encoded CT genes in somatic (non-germline) cells. CONCLUSION These findings confirm that a subset of CT genes can be regulated by hypomethylating drugs and subsequently provide a potential therapeutic target for cancer.
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Affiliation(s)
- Mikhlid H. Almutairi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Turki M. Alrubie
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Bader O. Almutairi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdullah M. Alamri
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdulwahed F. Alrefaei
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Maha M. Arafah
- Pathology Department, College of Medicine, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Alanazi
- Genome Research Chair, Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Abdelhabib Semlali
- Groupe de Recherche en Écologie Buccale, Faculté de Médecine Dentaire, Université Laval, 2420 Rue de la Terrasse, Local 1758, Québec, QC G1V 0A6, Canada
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Almutairi MH, Alotaibi MM, Alonaizan R, Almutairi BO. Expression Profile of MAGE-B1 Gene and Its Hypomethylation Activation in Colon Cancer. BIOMED RESEARCH INTERNATIONAL 2022; 2022:6066567. [PMID: 35937396 PMCID: PMC9348940 DOI: 10.1155/2022/6066567] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/04/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022]
Abstract
Cancer-testis (CT) genes are typically expressed in the testes; however, they have been linked to aberrant expression in a variety of malignancies. MAGE-B family genes are an example of CT genes. Therefore, the overarching objective of this study was to examine the expressions of MAGE-B family genes in several patients with colon cancer (CC) to see if they might be employed as cancer biomarkers in the early phases of cancer detection and to improve treatment. In this investigation, RT-PCR was used to analyze MAGE-B family genes in neighboring normal colon (NC) tissue from 10 CC patients. In addition, the effect of DNA demethylation on the expression status of the MAGE-B1 gene was evaluated by RT-PCR in HCT116 and Caco-2 cells and by qRT-PCR for HCT116 only after treating both CC cell lines with varying concentrations of 5-aza-2'-deoxycytidine (1.0, 5.0, and 10.0 μM) for 48 or 72 hours. All MAGE-B family genes except for MAGE-B1 showed weak bands in several samples of NC tissues: MAGE-B2, MAGE-B3, MAGE-B4, MAGE-B5, and MAGE-B6 genes were observed in 40%, 50%, 40%, 30%, and 60% of the NC samples, respectively. Nonetheless, they had strong bands in multiple samples of CC tissues, with 70%, 90%, 60%, 50%, and 90% of the CC samples, respectively. Interestingly, MAGE-B1 was detected in 60% of CC tissues but not in NC tissues, suggesting that it is a potential biomarker for early CC detection. MAGE-B1 expression was not observed in either untreated or DMSO-treated HCT116 cells after 48 or 72 hours of treatment. However, according to the RT-PCR and qRT-PCR results, the MAGE-B1 gene was overexpressed in the HCT116 cells treated with three different concentrations of 5-aza-2'-deoxycytidine. This shows that demethylation plays a crucial role in MAGE-B1 expression activation.
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Affiliation(s)
- Mikhlid H. Almutairi
- Zoology Department, College of Science, King Saud University, P.O. Box: 2455, 11451 Riyadh, Saudi Arabia
| | - Mona M. Alotaibi
- Zoology Department, College of Science, King Saud University, P.O. Box: 2455, 11451 Riyadh, Saudi Arabia
| | - Rasha Alonaizan
- Zoology Department, College of Science, King Saud University, P.O. Box: 2455, 11451 Riyadh, Saudi Arabia
| | - Bader O. Almutairi
- Zoology Department, College of Science, King Saud University, P.O. Box: 2455, 11451 Riyadh, Saudi Arabia
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Cancer-Testis Gene Biomarkers Discovered in Colon Cancer Patients. Genes (Basel) 2022; 13:genes13050807. [PMID: 35627192 PMCID: PMC9141640 DOI: 10.3390/genes13050807] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 04/23/2022] [Accepted: 04/28/2022] [Indexed: 12/04/2022] Open
Abstract
In Saudi Arabia, colon cancer (CC) is the most prevalent cancer in men and the third most common cancer in women. Rather than being detected through screening programs, most CC cases are diagnosed mainly during clinical exams. Because of the slow growth of CC and its ability to be treated at an early stage, screening for CC can reduce the incidence of death and mortality. Consequently, there is an urgent need to identify a potential new cancer-specific biomarker for detecting early illness. Much research has been conducted on distinct antigen classes as potential new cancer-specific biomarkers for the early identification of malignancy. The cancer-testis antigens (CTAs) are one such category of antigens, with protein presence largely normally confined to human germ line cells in the testis and aberrantly produced in some cancer cells. CTAs are potentially valuable for use as cancer biomarkers and in cancer therapeutics due to their distinctive expression pattern. The aim of this current study was to identify potential cancer-testis (CT) gene biomarkers in Saudi Arabian CC patients. In this study, a total of 20 matching CC and normal colon (NC) tissues were obtained from the Saudi population. Any genes that showed expression in CC tissues but not in matching NC tissues were subsequently verified for mRNA expression in eight breast and eight leukemia malignancies using RT-PCR to determine the specificity of any CC biomarkers. CTAG1A, SPZ1, LYZL6, SCP2D1, TEX33, and TKTL2 genes were expressed in varying numbers of CC tissues compared to no measurable expressions in all NC tissue specimens, making these genes suitable potential candidates for CC markers. The most frequently expressed CT genes in CC patients were CTAG1A (35%) and SCP2D1 (35%), followed by TKTL2 (25%), SPZ1 (20%), LYZL6 (15%), and TEX33 (5%). The LYZL6 gene shows a weak RT-PCR product in 25% of breast cancer (BC) patients but not in leukemia patients. The SCP2D1 gene appears to display expression in all leukemia patients but not in the BC patients. TKTL2 expression was also observed in 50% of leukemia samples but not in the BC samples. More experiments at the protein level and with a larger cohort of patients are required to evaluate this finding.
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Seelan RS, Mukhopadhyay P, Pisano MM, Greene RM. Effects of 5-Aza-2'-deoxycytidine (decitabine) on gene expression. Drug Metab Rev 2018; 50:193-207. [PMID: 29455551 DOI: 10.1080/03602532.2018.1437446] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
5-Aza-2'-deoxycytidine (AzaD), also known as Decitabine, is a deoxycytidine analog that is typically used to activate methylated and silenced genes by promoter demethylation. However, a survey of the scientific literature indicates that promoter demethylation may not be the only (or, indeed, the major) mechanism by which AzaD affects gene expression. Regulation of gene expression by AzaD can occur in several ways, including some that are independent of DNA demethylation. Results from several studies indicate that the effect of AzaD on gene expression is highly context-dependent and can differ for the same gene under different environmental settings. This may, in part, be due to the nature of the silencing mechanism(s) involved - DNA methylation, repressive histone modifications, or a combination of both. The varied effects of AzaD on such context-dependent regulation of gene expression may underlie some of the diverse responses exhibited by patients undergoing AzaD therapy. In this review, we describe the salient properties of AzaD with particular emphasis on its diverse effects on gene expression, aspects that have barely been discussed in most reviews of this interesting drug.
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Affiliation(s)
- Ratnam S Seelan
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
| | - Partha Mukhopadhyay
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
| | - M Michele Pisano
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
| | - Robert M Greene
- a Department of Surgical and Hospital Dentistry, Division of Craniofacial Development and Anomalies , ULSD, University of Louisville , Louisville , KY , USA
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Lei Q, Liu X, Fu H, Sun Y, Wang L, Xu G, Wang W, Yu Z, Liu C, Li P, Feng J, Li G, Wu M. miR-101 reverses hypomethylation of the PRDM16 promoter to disrupt mitochondrial function in astrocytoma cells. Oncotarget 2016; 7:5007-22. [PMID: 26701852 PMCID: PMC4826261 DOI: 10.18632/oncotarget.6652] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 12/05/2015] [Indexed: 01/17/2023] Open
Abstract
Our previous report identified PR domain containing 16 (PRDM16), a member of the PR-domain gene family, as a new methylation associated gene in astrocytoma cells. This previous study also reported that miR-101 is a tumor suppressor in glioma. The present study confirms that PRDM16 is a hypomethylated gene that can be overexpressed in astrocytoma patients and demonstrates that the hypomethylation status of the PRDM16 promoter can predict poor prognoses for astrocytoma patients. The results reported herein show that PRDM16 was inhibited by miR-101 directly and also through epigenetic regulation. PRDM16 was confirmed as a new target of miR-101 and shown to be directly inhibited by miR-101. miR-101 also decreased the expression of PRDM16 by altering the methylation status of the PRDM16 promoter. miR-101 was associated with a decrease in the methylation-related histones H3K4me2 and H3K27me3 and an increase in H3K9me3 and H4K20me3 on the PRDM16 promoter. In addition, EZH2, EED and DNMT3A were identified as direct targets of miR-101, and miR-101 suppressed PRDM16 expression by targeting DNMT3A which decreases histone H3K27me3 and H3K4me2 at the PRDM16 core promoter. The results reported here demonstrate that miR-101 disrupted cellular mitochondrial function and induced cellular apoptosis via the mitochondrial pathway; for example, MMP and ATP levels decreased, while there was an increase in ADP/ATP ratios and ROS levels, levels of cleaved Caspase-9 and cleaved-PARP, the Bax/Bcl-2 ratios, and Smac release from the mitochondria to the cytoplasm. Knockdown of PRDM16 reversed the anti-apoptotic effect of miR-101 inhibition. In summary, miR-101 reversed the hypomethylation of the PRDM16 promoter which suppressed the expression of PRDM16, disrupted cellular mitochondrial function, and induced cellular apoptosis.
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Affiliation(s)
- Qianqian Lei
- Hunan Provincial Tumor Hospital and The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha 410013, Hunan, China.,Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha 410078, Hunan, China
| | - Xiaoping Liu
- Department of Breast Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, Guangdong, China
| | - Haijuan Fu
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha 410078, Hunan, China
| | - Yingnan Sun
- Hunan Provincial Tumor Hospital and The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha 410013, Hunan, China.,Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha 410078, Hunan, China
| | - Liping Wang
- Department of Oncology, The First Hospital of Chenzhou City, 423000, Hunan, China
| | - Gang Xu
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha 410078, Hunan, China
| | - Wei Wang
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha 410078, Hunan, China
| | - Zhibin Yu
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha 410078, Hunan, China
| | - Changhong Liu
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha 410078, Hunan, China
| | - Peiyao Li
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha 410078, Hunan, China
| | - Jianbo Feng
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha 410078, Hunan, China
| | - Guiyuan Li
- Hunan Provincial Tumor Hospital and The Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha 410013, Hunan, China.,Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha 410078, Hunan, China
| | - Minghua Wu
- Cancer Research Institute, School of Basic Medical Science, Central South University, Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Key Laboratory of Carcinogenesis, Ministry of Health, Changsha 410078, Hunan, China
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Deibel SH, Zelinski EL, Keeley RJ, Kovalchuk O, McDonald RJ. Epigenetic alterations in the suprachiasmatic nucleus and hippocampus contribute to age-related cognitive decline. Oncotarget 2016; 6:23181-203. [PMID: 26252151 PMCID: PMC4695111 DOI: 10.18632/oncotarget.4036] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 12/31/1969] [Indexed: 12/16/2022] Open
Abstract
Circadian rhythm dysfunction and cognitive decline, specifically memory loss, frequently accompany natural aging. Circadian rhythms and memory are intertwined, as circadian rhythms influence memory formation and recall in young and old rodents. Although, the precise relationship between circadian rhythms and memory is still largely unknown, it is hypothesized that circadian rhythm disruption, which occurs during aging, contributes to age-associated cognitive decline, specifically memory loss. While there are a variety of mechanisms that could mediate this effect, changes in the epigenome that occur during aging has been proposed as a potential candidate. Interestingly, epigenetic mechanisms, such as DNA methylation and sirtuin1 (SIRT1) are necessary for both circadian rhythms and memory. During aging, similar alterations of epigenetic mechanisms occur in the suprachiasmatic nucleus (SCN) and hippocampus, which are necessary for circadian rhythm generation and memory, respectively. Recently, circadian rhythms have been linked to epigenetic function in the hippocampus, as some of these epigenetic mechanisms oscillate in the hippocampus and are disrupted by clock gene deletion. The current paper will review how circadian rhythms and memory change with age, and will suggest how epigenetic changes in these processes might contribute to age-related cognitive decline.
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Affiliation(s)
- Scott H Deibel
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Erin L Zelinski
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Robin J Keeley
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
| | - Robert J McDonald
- Canadian Centre for Behavioural Neuroscience, Department of Neuroscience, University of Lethbridge, Lethbridge, AB, Canada
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Gumireddy K, Li A, Chang DH, Liu Q, Kossenkov AV, Yan J, Korst RJ, Nam BT, Xu H, Zhang L, Ganepola GAP, Showe LC, Huang Q. AKAP4 is a circulating biomarker for non-small cell lung cancer. Oncotarget 2016; 6:17637-47. [PMID: 26160834 PMCID: PMC4627334 DOI: 10.18632/oncotarget.3946] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/01/2015] [Indexed: 12/18/2022] Open
Abstract
Cancer testis antigens (CTAs) are widely expressed in tumor tissues, circulating tumor cells (CTCs) and in cancer derived exosomes that are frequently engulfed by lymphoid cells. To determine whether tumor derived CTA mRNAs could be detected in RNA from purified peripheral blood mononuclear cells (PBMC) of non-small cell lung cancer (NSCLC) patients, we assayed for the expression of 116 CTAs in PBMC RNA in a discovery set and identified AKAP4 as a potential NSCLC biomarker. We validated AKAP4 as a highly accurate biomarker in a cohort of 264 NSCLCs and 135 controls from 2 different sites including a subset of controls with high risk lung nodules. When all (264) lung cancers were compared with all (135) controls the area under the ROC curve (AUC) was 0.9714. When 136 stage I NSCLC lung cancers are compared with all controls the AUC is 0.9795 and when all lung cancer patients were compared to 27 controls with histologically confirmed benign lung nodules, a comparison of significant clinical importance, the AUC was 0.9825. AKAP4 expression increases significantly with tumor stage, but independent of age, gender, smoking history or cancer subtype. Follow-up studies in a small number of resected NSCLC patients revealed a decrease of AKAP4 expression post-surgical resection that remained low in patients in remission and increased with tumor recurrence. AKAP4 is a highly accurate biomarker for the detection of early stage lung cancer.
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Affiliation(s)
| | - Anping Li
- The Wistar Institute Cancer Center, Philadelphia, PA 19104, USA
| | - David H Chang
- Center for Cancer Research and Genomic Medicine, The Valley Hospital, Paramus, NJ 07652, USA
| | - Qin Liu
- The Wistar Institute Cancer Center, Philadelphia, PA 19104, USA
| | | | - Jinchun Yan
- University of Washington Medical Center, Seattle, WA 98195, USA
| | - Robert J Korst
- Department of Surgery, The Valley Hospital, Ridgewood, NJ 07450, USA
| | - Brian T Nam
- Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE 19713, USA
| | - Hua Xu
- Department of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan 430030, China
| | - Lin Zhang
- Center for Research on Early Detection and Cure of Ovarian Cancer, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ganepola A P Ganepola
- Center for Cancer Research and Genomic Medicine, The Valley Hospital, Paramus, NJ 07652, USA.,Department of Surgery, The Valley Hospital, Ridgewood, NJ 07450, USA
| | - Louise C Showe
- The Wistar Institute Cancer Center, Philadelphia, PA 19104, USA
| | - Qihong Huang
- The Wistar Institute Cancer Center, Philadelphia, PA 19104, USA
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12
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Yang JJ, Tao H, Deng ZY, Lu C, Li J. Non-coding RNA-mediated epigenetic regulation of liver fibrosis. Metabolism 2015; 64:1386-94. [PMID: 26362725 DOI: 10.1016/j.metabol.2015.08.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 07/06/2015] [Accepted: 08/08/2015] [Indexed: 12/27/2022]
Abstract
Hepatic stellate cells (HSC) activation plays a key role in liver fibrosis. Numerous studies have indicated that non-coding RNAs (ncRNAs) control liver fibrosis and fibroblasts proliferation. Greater knowledge of the role of the ncRNAs-mediated epigenetic mechanism in liver fibrosis could improve understanding of the liver fibrosis pathogenesis. The aim of this review is to describe the present knowledge about the ncRNAs significantly participating in liver fibrosis and HSC activation, and look ahead on new perspectives of ncRNAs-mediated epigenetic mechanism research. Moreover, we will discuss examples of non-coding RNAs that interact with histone modification or DNA methylation to regulate gene expression in liver fibrosis. Diverse classes of ncRNAs, ranging from microRNAs (miRs) to long non-coding RNAs (LncRNAs), have emerged as key regulators of several important aspects of function, including cell proliferation, activation, etc. In addition, recent advances suggest the important role of ncRNAs transcripts in epigenetic gene regulation. Targeting the miRs and LncRNAs can be a promising direction in liver fibrosis treatment. We discuss new perspectives of miRs and LncRNAs in liver fibrosis and HSC activation, mainly including interaction with histone modification or DNA methylation to regulate gene expression. These epigenetic mechanisms form powerful ncRNAs surveillance systems that may represent new targets for liver fibrosis therapeutic intervention.
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Affiliation(s)
- Jing-Jing Yang
- Department of Pharmacology, The Second Hospital of Anhui Medical University, Hefei, China, 230601
| | - Hui Tao
- Department of Cardiothoracic Surgery, The Second Hospital of Anhui Medical University, Hefei, China, 230601
| | - Zi-Yu Deng
- Department of Scientific and Educational, The Second Hospital of Anhui Medical University, Hefei, China, 230601.
| | - Chao Lu
- Department of Scientific and Educational, The Second Hospital of Anhui Medical University, Hefei, China, 230601
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Hefei, China, 230032.
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13
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McFarlane RJ, Feichtinger J, Larcombe L. Germline/meiotic genes in cancer: new dimensions. Cell Cycle 2015; 14:791-2. [PMID: 25790090 PMCID: PMC4614398 DOI: 10.1080/15384101.2015.1010965] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Revised: 01/10/2015] [Accepted: 01/14/2015] [Indexed: 10/22/2022] Open
Affiliation(s)
- Ramsay J McFarlane
- North West Cancer Research Institute; School of Medical Sciences; Bangor University; Bangor, UK
| | - Julia Feichtinger
- Institute for Knowledge Discovery; Graz University of Technology; Graz, Austria
- Core Facility Bioinformatics; Austrian Center of Industrial Biotechnology; Graz, Austria
| | - Lee Larcombe
- MRC Functional Genomics Unit; Department of Physiology; Anatomy and Genetics; University of Oxford; Oxford, UK
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