1
|
Alimohammadi M, Rahimzadeh P, Khorrami R, Bonyadi M, Daneshi S, Nabavi N, Raesi R, Farani MR, Dehkhoda F, Taheriazam A, Hashemi M. A comprehensive review of the PTEN/PI3K/Akt axis in multiple myeloma: From molecular interactions to potential therapeutic targets. Pathol Res Pract 2024; 260:155401. [PMID: 38936094 DOI: 10.1016/j.prp.2024.155401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 06/02/2024] [Accepted: 06/09/2024] [Indexed: 06/29/2024]
Abstract
Phosphatase and tensin homolog (PTEN), phosphatidylinositol 3-kinase (PI3K), and protein kinase B (Akt) signaling pathways contribute to the development of several cancers, including multiple myeloma (MM). PTEN is a tumor suppressor that influences the PI3K/Akt/mTOR pathway, which in turn impacts vital cellular processes like growth, survival, and treatment resistance. The current study aims to present the role of PTEN and PI3K/Akt/mTOR signaling in the development of MM and its response to treatment. In addition, the molecular interactions in MM that underpin the PI3K/Akt/mTOR pathway and address potential implications for the development of successful treatment plans are also discussed in detail. We investigate their relationship to both upstream and downstream regulators, highlighting new developments in combined therapies that target the PTEN/PI3K/Akt axis to overcome drug resistance, including the use of PI3K and mitogen-activated protein kinase (MAPK) inhibitors. We also emphasize that PTEN/PI3K/Akt pathway elements may be used in MM diagnosis, prognosis, and therapeutic targets.
Collapse
Affiliation(s)
- Mina Alimohammadi
- Department of Immunology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran.
| | - Payman Rahimzadeh
- Surgical Research Society (SRS), Students' Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ramin Khorrami
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Islamic Republic of Iran
| | - Mojtaba Bonyadi
- Department of Food Hygiene and Quality Control, Faculty of Veterinary Medicine, University of Tehran, Tehran, Islamic Republic of Iran
| | - Salman Daneshi
- Department of Public Health, School of Health, Jiroft University of Medical Sciences, Jiroft, Islamic Republic of Iran
| | - Noushin Nabavi
- Independent Researcher, Victoria, British Columbia V8V 1P7, Canada
| | - Rasoul Raesi
- Department of Health Services Management, Mashhad University of Medical Sciences, Mashhad, Islamic Republic of Iran; Department of Nursing, Torbat Jam Faculty of Medical Sciences, Torbat Jam, Iran
| | - Marzieh Ramezani Farani
- NanoBio High-Tech Materials Research Center, Department of Biological Sciences and Bioengineering, Inha University, 100 Inha-ro, Incheon 22212, Republic of Korea
| | - Farshid Dehkhoda
- Department of Orthopedics, Shahid Beheshti University of Medical Sciences, Tehran, Islamic Republic of Iran.
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Islamic Republic of Iran; Department of Orthopedics, Faculty of Medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Islamic Republic of Iran.
| | - Mehrdad Hashemi
- Farhikhtegan Medical Convergence Sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Islamic Republic of Iran; Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Islamic Republic of Iran.
| |
Collapse
|
2
|
Han Y, Meng J, Ling X, Pan Z, Zhang H, Zhong B, Chen S, Pang J, Ma Y, Chen J, Liu L. DNMT1 regulates hypermethylation and silences hsa_circ_401351 in hydroquinone-induced malignant TK6 cells. ENVIRONMENTAL TOXICOLOGY 2024; 39:2092-2101. [PMID: 38108535 DOI: 10.1002/tox.24089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 11/18/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023]
Abstract
BACKGROUND Benzene and its metabolite hydroquinone (HQ) are widely used in daily life, and long-term exposure to benzene or HQ can induce acute myeloid leukemia (AML). Circular RNAs (circRNAs) are mostly produced by reverse splicing of gene exon mRNA precursors. The modulation of circRNA expression is connected to leukemia progression; however, the molecular mechanism is still unknown. MATERIALS AND METHODS In this study, the cells were divided into four groups: PBS control group (PBS-TK6), TK6 malignantly transformed cells induced by 10.0 μmol/L HQ (HQ-TK6), and HQ-TK6 cells treated with 5 μmol/L 5-AzaC (DNA methyltransferase inhibitor) for 24 h (HQ + 5-AzaC). HQ-TK6 cells were treated with 200 nmol/L TSA (histone deacetylation inhibitor) for 24 h (HQ + TSA). qRT-PCR was used to identify the differential hsa_circ_401351 expression between the four groups. We further determined the hsa_circ_401351 promoter methylation level with methylation-specific PCR. DNMT1 and DNMT3b were knocked down by CRISPR/Cas9 to elucidate the specific molecular mechanism of hsa_circ_401351 in HQ-TK6 cells. CCK-8 and flow cytometry detected cell proliferation and apoptosis, respectively, after hsa_circ_401351 was overexpressed in HQ-TK6 cells. RESULTS Compared with the PBS-TK6 group, the expression of hsa_circ_401351 was found to be lower in the HQ-TK6 group. Nevertheless, treatment with 5-AzaC or TSA increased hsa_circ_401351 expression, with the upregulation being more pronounced in the TSA group. The expression of hsa_circ_401351 in the DNMT1 knockdown group was dramatically increased by 50% compared to that in the control group, and the DNA methylation level of the hsa_circ_401351 promoter region was decreased. When hsa_circ_401351 was overexpressed, HQ-TK6 cell proliferation was significantly slowed after 48 h compared with the control group. Flow cytometry showed that cells were mainly arrested in G1 phase, and apoptosis was significantly enhanced. Similarly, qRT-PCR and Western blot data showed significant reductions in Caspase-3 mRNA and protein production, and Bcl-2 mRNA levels were also elevated. CONCLUSIONS Overall, our research showed that elevated DNMT1 expression in HQ-TK6 cells increased methylation levels and decreased expression of the hsa_circ_401351 promoter region, limiting its ability to suppress HQ-TK6 cell growth and enhance apoptosis.
Collapse
Affiliation(s)
- Yali Han
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
| | - Jinxue Meng
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
| | - Xiaoxuan Ling
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
| | - Zhijie Pan
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
| | - Haiqiao Zhang
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
- Department of Hospital Infection Management, Dongguan Maternal and Child Health Care Hospital, Dongguan, People's Republic of China
| | - Bohuan Zhong
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
| | - Shi Chen
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
| | - Jing Pang
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
| | - Yuliang Ma
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
| | - Jialong Chen
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
| | - Linhua Liu
- Dongguan Key Laboratory of Environmental Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
- Department of Preventive Medicine, School of Public Health, Guangdong Medical University, Dongguan, People's Republic of China
| |
Collapse
|
3
|
Deycmar S, Johnson BJ, Ray K, Schaaf GW, Ryan DP, Cullin C, Dozier BL, Ferguson B, Bimber BN, Olson JD, Caudell DL, Whitlow CT, Solingapuram Sai KK, Romero EC, Villinger FJ, Burgos AG, Ainsworth HC, Miller LD, Hawkins GA, Chou JW, Gomes B, Hettich M, Ceppi M, Charo J, Cline JM. Epigenetic MLH1 silencing concurs with mismatch repair deficiency in sporadic, naturally occurring colorectal cancer in rhesus macaques. J Transl Med 2024; 22:292. [PMID: 38504345 PMCID: PMC10953092 DOI: 10.1186/s12967-024-04869-6] [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: 08/25/2023] [Accepted: 01/08/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Naturally occurring colorectal cancers (CRC) in rhesus macaques share many features with their human counterparts and are useful models for cancer immunotherapy; but mechanistic data are lacking regarding the comparative molecular pathogenesis of these cancers. METHODS We conducted state-of-the-art imaging including CT and PET, clinical assessments, and pathological review of 24 rhesus macaques with naturally occurring CRC. Additionally, we molecularly characterized these tumors utilizing immunohistochemistry (IHC), microsatellite instability assays, DNAseq, transcriptomics, and developed a DNA methylation-specific qPCR assay for MLH1, CACNA1G, CDKN2A, CRABP1, and NEUROG1, human markers for CpG island methylator phenotype (CIMP). We furthermore employed Monte-Carlo simulations to in-silico model alterations in DNA topology in transcription-factor binding site-rich promoter regions upon experimentally demonstrated DNA methylation. RESULTS Similar cancer histology, progression patterns, and co-morbidities could be observed in rhesus as reported for human CRC patients. IHC identified loss of MLH1 and PMS2 in all cases, with functional microsatellite instability. DNA sequencing revealed the close genetic relatedness to human CRCs, including a similar mutational signature, chromosomal instability, and functionally-relevant mutations affecting KRAS (G12D), TP53 (R175H, R273*), APC, AMER1, ALK, and ARID1A. Interestingly, MLH1 mutations were rarely identified on a somatic or germline level. Transcriptomics not only corroborated the similarities of rhesus and human CRCs, but also demonstrated the significant downregulation of MLH1 but not MSH2, MSH6, or PMS2 in rhesus CRCs. Methylation-specific qPCR suggested CIMP-positivity in 9/16 rhesus CRCs, but all 16/16 exhibited significant MLH1 promoter hypermethylation. DNA hypermethylation was modelled to affect DNA topology, particularly propeller twist and roll profiles. Modelling the DNA topology of a transcription factor binding motif (TFAP2A) in the MLH1 promoter that overlapped with a methylation-specific probe, we observed significant differences in DNA topology upon experimentally shown DNA methylation. This suggests a role of transcription factor binding interference in epigenetic silencing of MLH1 in rhesus CRCs. CONCLUSIONS These data indicate that epigenetic silencing suppresses MLH1 transcription, induces the loss of MLH1 protein, abrogates mismatch repair, and drives genomic instability in naturally occurring CRC in rhesus macaques. We consider this spontaneous, uninduced CRC in immunocompetent, treatment-naïve rhesus macaques to be a uniquely informative model for human CRC.
Collapse
Affiliation(s)
- Simon Deycmar
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Roche Postdoctoral Fellowship (RPF) Program, Basel, Switzerland
| | - Brendan J Johnson
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Karina Ray
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - George W Schaaf
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Declan Patrick Ryan
- School of Veterinary Medicine, University of California Davis, Davis, CA, USA
| | - Cassandra Cullin
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Brandy L Dozier
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Betsy Ferguson
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - Benjamin N Bimber
- Oregon National Primate Research Center, Oregon Health and Science University, Beaverton, OR, USA
| | - John D Olson
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - David L Caudell
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Christopher T Whitlow
- Department of Radiology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | | | - Emily C Romero
- New Iberia Research Center, University of Louisiana-Lafayette, New Iberia, LA, USA
| | - Francois J Villinger
- New Iberia Research Center, University of Louisiana-Lafayette, New Iberia, LA, USA
| | - Armando G Burgos
- Caribbean Primate Research Center, University of Puerto Rico, Toa Baja, PR, USA
| | - Hannah C Ainsworth
- Department of Biostatistics and Data Sciences, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Lance D Miller
- Department of Cancer Biology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Center for Cancer Genomics and Precision Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Gregory A Hawkins
- Center for Cancer Genomics and Precision Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Jeff W Chou
- Center for Cancer Genomics and Precision Oncology, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Bruno Gomes
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Michael Hettich
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
| | - Maurizio Ceppi
- Roche Pharma Research and Early Development, Roche Innovation Center Basel, Basel, Switzerland
- iTeos Therapeutics, Translational Medicine, Gosselies, Belgium
| | - Jehad Charo
- Roche Pharma Research and Early Development, Roche Innovation Center Zurich, Zurich, Switzerland
| | - J Mark Cline
- Department of Pathology, Wake Forest University School of Medicine, Winston-Salem, NC, USA.
| |
Collapse
|
4
|
de Boer CG, Taipale J. Hold out the genome: a roadmap to solving the cis-regulatory code. Nature 2024; 625:41-50. [PMID: 38093018 DOI: 10.1038/s41586-023-06661-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 09/20/2023] [Indexed: 01/05/2024]
Abstract
Gene expression is regulated by transcription factors that work together to read cis-regulatory DNA sequences. The 'cis-regulatory code' - how cells interpret DNA sequences to determine when, where and how much genes should be expressed - has proven to be exceedingly complex. Recently, advances in the scale and resolution of functional genomics assays and machine learning have enabled substantial progress towards deciphering this code. However, the cis-regulatory code will probably never be solved if models are trained only on genomic sequences; regions of homology can easily lead to overestimation of predictive performance, and our genome is too short and has insufficient sequence diversity to learn all relevant parameters. Fortunately, randomly synthesized DNA sequences enable testing a far larger sequence space than exists in our genomes, and designed DNA sequences enable targeted queries to maximally improve the models. As the same biochemical principles are used to interpret DNA regardless of its source, models trained on these synthetic data can predict genomic activity, often better than genome-trained models. Here we provide an outlook on the field, and propose a roadmap towards solving the cis-regulatory code by a combination of machine learning and massively parallel assays using synthetic DNA.
Collapse
Affiliation(s)
- Carl G de Boer
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Jussi Taipale
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
| |
Collapse
|
5
|
Sharma S, Bhonde R. Applicability of mesenchymal stem cell-derived exosomes as a cell-free miRNA therapy and epigenetic modifiers for diabetes. Epigenomics 2023; 15:1323-1336. [PMID: 38018455 DOI: 10.2217/epi-2023-0302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023] Open
Abstract
Given that exosome nanovesicles constitute various growth factors, miRNAs and lncRNAs, they have implications for epigenetic modifications. Few studies have shown that exosomes from mesenchymal stem cells (MSCs) exhibit therapeutic effects on diabetic complications by substituting miRNAs and regulating histone modifications. Therefore, reversing epigenetic aberrations in diabetes may provide new insight into its treatment. This review discusses the impact of DNA and histone methylations on the development of diabetes and its complications. Further, we talk about miRNAs dysregulated in diabetic conditions and the possibility of utilizing mesenchymal stem cell (MSC) exosomes for the development of miRNA cell-free therapy and epigenetic modifiers in reversing diabetic-induced epigenetic alterations.
Collapse
Affiliation(s)
- Shikha Sharma
- Institute For Stem Cell Science & Regenerative Medicine, Bangalore, 560065, India
| | - Ramesh Bhonde
- Dr D.Y. Patil Vidyapeeth, Pimpri, Pune, 411018, India
| |
Collapse
|
6
|
Guo X, Wang Y, Zha L, Li H, Qian K. DNA methylation-related lncRNAs predict prognosis and immunotherapy response in gastric cancer. J Cancer Res Clin Oncol 2023; 149:14745-14760. [PMID: 37592033 DOI: 10.1007/s00432-023-05234-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/31/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND LncRNAs and DNA methylation are both key regulators of tumorigenesis and immune regulation. However, the interaction between lncRNA and DNA methylation, their regulation and their clinical and immune relevance in gastric cancer (GC) remain unclear. METHODS In this study, we identified DNA methylation regulator-related lncRNAs through Pearson correlation analysis in The Cancer Genome Atlas datasets. Univariate Cox regression was used to screen DNA methylationrelated prognostic lncRNAs. Further, through least absolute shrinkage and selection operator Cox regression, a prognostic model based on 13 lncRNAs was established. Survival analysis and receiver operating characteristic curve analysis verified the accuracy of the model in predicting the survival of GC patients. Univariate and multivariate analyses also confirmed that the risk score obtained from the risk model could be applied as an independent prognostic factor for patients with GC. Furthermore, based on the risk score and other clinicopathological characteristics that can be used as independent prognostic factors, we constructed a nomogram that could accurately determine the survival time of each patient. In addition, a lncRNA score was constructed using a principal component analysis algorithm to quantify the DNA methylation-related lncRNA expression patterns of individual tumors. RESULTS We found that a higher lncRNA score indicated a worse the prognosis and was associated with a reduced tumor mutation burden and immunosuppression. A low lncRNA score was related to an increase in neoantigen load and an increase in the anti-PDL1/CTLA4 immunotherapy response. Additionally, a low lncRNA score was related to a significant therapeutic advantage and clinical benefit. CONCLUSIONS This study describes a DNA methylation regulator-related lncRNA signature model, which provides a new approach for predicting therapeutic response and patient stratification in GC. Assessing lncRNA expression patterns in individual tumors will contribute to enhancing our understanding of tumor microenvironment infiltration and guide more effective immunotherapy strategies.
Collapse
Affiliation(s)
- Xiong Guo
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
| | - Yujun Wang
- Department of Pathology, Daping Hospital, Army Military Medical University, Chongqing, 400042, People's Republic of China
| | - Lang Zha
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
| | - Hui Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China
| | - Kun Qian
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Chongqing Medical University, Chongqing, 400010, People's Republic of China.
| |
Collapse
|
7
|
Patnaik E, Madu C, Lu Y. Epigenetic Modulators as Therapeutic Agents in Cancer. Int J Mol Sci 2023; 24:14964. [PMID: 37834411 PMCID: PMC10573652 DOI: 10.3390/ijms241914964] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 10/04/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Epigenetics play a crucial role in gene regulation and cellular processes. Most importantly, its dysregulation can contribute to the development of tumors. Epigenetic modifications, such as DNA methylation and histone acetylation, are reversible processes that can be utilized as targets for therapeutic intervention. DNA methylation inhibitors disrupt DNA methylation patterns by inhibiting DNA methyltransferases. Such inhibitors can restore normal gene expression patterns, and they can be effective against various forms of cancer. Histone deacetylase inhibitors increase histone acetylation levels, leading to altered gene expressions. Like DNA methylation inhibitors, histone methyltransferase inhibitors target molecules involved in histone methylation. Bromodomain and extra-terminal domain inhibitors target proteins involved in gene expression. They can be effective by inhibiting oncogene expression and inducing anti-proliferative effects seen in cancer. Understanding epigenetic modifications and utilizing epigenetic inhibitors will offer new possibilities for cancer research.
Collapse
Affiliation(s)
- Eshaan Patnaik
- Department of Biology, Memphis University School, Memphis, TN 38119, USA;
| | - Chikezie Madu
- Departments of Biological Sciences, University of Memphis, Memphis, TN 38152, USA;
| | - Yi Lu
- Department of Pathology and Laboratory Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| |
Collapse
|
8
|
Hadziselimovic F, Verkauskas G, Stadler MB. Epigenetics, cryptorchidism, and infertility. Basic Clin Androl 2023; 33:24. [PMID: 37730534 PMCID: PMC10512650 DOI: 10.1186/s12610-023-00199-7] [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: 04/05/2023] [Accepted: 06/02/2023] [Indexed: 09/22/2023] Open
Abstract
BACKGROUND Cryptorchid boys with defective mini-puberty and impaired differentiation of Ad spermatogonia (high infertility risk) have altered expression of several genes encoding histone methyltransferases compared to patients with intact differentiation of gonocytes into Ad spermatogonia (low infertility risk). RESULTS High infertility risk cryptorchid boys display hypogonadotropic hypogonadism, which, together with the diminished expression of histone deacetylases and increased expression of HDAC8 decrotonylase, indicates altered histone marks and, thus, a perturbed histone code. Curative GnRHa treatment induces normalization of histone methyltransferase, chromatin remodeling, and histone deacetylase gene expression. As a result, histone changes induce differentiation of Ad spermatogonia from their precursors and, thus, fertility. In this short report, we describe key functions of histone lysine methyltransferases, chromatin remodeling proteins, and long-noncoding RNAs, and discuss their potential roles in processes leading to infertility. CONCLUSION Our findings suggest that epigenetic mechanisms are critical to better understanding the root causes underlying male infertility related to cryptorchidism and its possible transgenerational transmission.
Collapse
Affiliation(s)
- Faruk Hadziselimovic
- Cryptorchidism Research Institute, Children’s Day Care Center, 4410 Liestal, Switzerland
| | - Gilvydas Verkauskas
- Children’s Surgery Centre, Faculty of Medicine, Vilnius University, 01513 Vilnius, Lithuania
| | - Michael B. Stadler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| |
Collapse
|
9
|
Zhang H, Wu T, Ren C, Dong N, Wu Y, Yao Y. p53 promotes the expansion of regulatory T cells via DNMT3a- and TET2- mediated Foxp3 expression in sepsis. BURNS & TRAUMA 2023; 11:tkad021. [PMID: 37564681 PMCID: PMC10410290 DOI: 10.1093/burnst/tkad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/13/2023] [Accepted: 03/24/2023] [Indexed: 08/12/2023]
Abstract
Background Immunosuppression is an important characteristic of sepsis and is closely related to poor outcomes. Regulatory T cells (Tregs) contribute to immune suppression by inhibiting effector T cell (Teff) proliferation and differentiation. We aimed to investigate the role of p53 in Treg expansion after sepsis. Methods We constructed a sepsis model in wild-type (WT) and p53f/f/CD4-Cre+ mice by cecal ligation and puncture (CLP) and evaluated the proportions of CD4+CD25+ Foxp3+ Tregs by flow cytometry. The expression levels of forkhead/winged helix transcription factor p3 (Foxp3), DNA methyltransferase enzyme (DMNT)3a and ten-eleven translocation (TET)2 were examined using quantitative real-time PCR and Western blot analysis. Treg-specific demethylation region (TSDR) methylation sites in cells were analyzed by bisulfite-sequencing PCR. Furthermore, the direct binding of p53 to the Dnmt3a and TET2 promoters was illustrated using a luciferase assay. The suppressive ability of Tregs was indicated by enzyme-linked immunosorbent assay analysis of cytokine levels and the proliferation of cocultured Teffs. Finally, mortality rates after CLP were compared among WT and p53f/f/CD4-Cre+ mice. Results The proportion of CD4+CD25+ Foxp3+ Tregs was significantly reduced in p53f/f/CD4-Cre+ mice compared to WT mice after CLP. The enhanced expression of Foxp3 in WT mice was downregulated in the p53f/f/CD4-Cre+ group. We found decreased DMNT3a and increased TET2 levels after CLP. However, the dysregulation of DNMT3a and TET2 was significantly reversed in p53f/f/CD4-Cre+ mice. TSDR underwent increased demethylation in p53f/f/CD4-Cre+ mice. Luciferase activity indicated direct binding of p53 to the promoter regions of DNMT3a and TET2 to regulate their transcription. Consequently, Tregs from p53f/f/CD4-Cre+ CLP mice exhibited limited suppressive ability, as indicated by the reduced production of transforming growth factor-β and interleukin 10 (IL-10). In the coculture system, Teffs showed preserved production of IL-2, differentiation into Th1 cells and proliferation in the presence of Tregs isolated from p53f/f/CD4-Cre+ CLP mice. Finally, the mortality rate of the p53f/f/CD4-Cre+ group after CLP was significantly reduced in comparison to that of the WT group. Conclusion p53 appears to be critical for Foxp3 expression and consequent Treg expansion by regulating the induction of DNMT3a and TET2, thereby resulting in Foxp3-TSDR demethylation in the context of sepsis.
Collapse
Affiliation(s)
- Hui Zhang
- Translational Medicine Research Center, Medical Innovation Research Division and Fourth Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Tiantian Wu
- Department of Hepatobiliary Surgery, Peking University International Hospital, No. 1 Science Park Road, Life Science Park, Changping District, Beijing 100034, People’s Republic of China
| | - Chao Ren
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine, Beijing Chao-Yang Hospital, Capital Medical University, No. 8 Worker's Stadium South Road, Chao-yang District, Beijing, China
| | - Ning Dong
- Translational Medicine Research Center, Medical Innovation Research Division and Fourth Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Yao Wu
- Translational Medicine Research Center, Medical Innovation Research Division and Fourth Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Yongming Yao
- Translational Medicine Research Center, Medical Innovation Research Division and Fourth Medical Center of the Chinese PLA General Hospital, Beijing, People’s Republic of China
| |
Collapse
|
10
|
Dave J, Jagana V, Janostiak R, Bisserier M. Unraveling the epigenetic landscape of pulmonary arterial hypertension: implications for personalized medicine development. J Transl Med 2023; 21:477. [PMID: 37461108 DOI: 10.1186/s12967-023-04339-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Pulmonary arterial hypertension (PAH) is a multifactorial disease associated with the remodeling of pulmonary blood vessels. If left unaddressed, PAH can lead to right heart failure and even death. Multiple biological processes, such as smooth muscle proliferation, endothelial dysfunction, inflammation, and resistance to apoptosis, are associated with PAH. Increasing evidence suggests that epigenetic factors play an important role in PAH by regulating the chromatin structure and altering the expression of critical genes. For example, aberrant DNA methylation and histone modifications such as histone acetylation and methylation have been observed in patients with PAH and are linked to vascular remodeling and pulmonary vascular dysfunction. In this review article, we provide a comprehensive overview of the role of key epigenetic targets in PAH pathogenesis, including DNA methyltransferase (DNMT), ten-eleven translocation enzymes (TET), switch-independent 3A (SIN3A), enhancer of zeste homolog 2 (EZH2), histone deacetylase (HDAC), and bromodomain-containing protein 4 (BRD4). Finally, we discuss the potential of multi-omics integration to better understand the molecular signature and profile of PAH patients and how this approach can help identify personalized treatment approaches.
Collapse
Affiliation(s)
- Jaydev Dave
- Department of Cell Biology and Anatomy, New York Medical College, 15 Dana Road, BSB 131A, Valhalla, NY, 10595, USA
- Department of Physiology, New York Medical College, 15 Dana Road, BSB 131A, Valhalla, NY, 10595, USA
| | - Vineeta Jagana
- Department of Cell Biology and Anatomy, New York Medical College, 15 Dana Road, BSB 131A, Valhalla, NY, 10595, USA
- Department of Physiology, New York Medical College, 15 Dana Road, BSB 131A, Valhalla, NY, 10595, USA
| | - Radoslav Janostiak
- First Faculty of Medicine, BIOCEV, Charles University, Vestec, 25250, Czech Republic
| | - Malik Bisserier
- Department of Cell Biology and Anatomy, New York Medical College, 15 Dana Road, BSB 131A, Valhalla, NY, 10595, USA.
- Department of Physiology, New York Medical College, 15 Dana Road, BSB 131A, Valhalla, NY, 10595, USA.
| |
Collapse
|
11
|
Sergeeva A, Davydova K, Perenkov A, Vedunova M. Mechanisms of human DNA methylation, alteration of methylation patterns in physiological processes and oncology. Gene 2023:147487. [PMID: 37211289 DOI: 10.1016/j.gene.2023.147487] [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: 03/02/2023] [Revised: 05/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
DNA methylation is one of the epigenetic modifications of the genome, the essence of which is the attachment of a methyl group to nitrogenous bases. In the eukaryote genome, cytosine is methylated in the vast majority of cases. About 98% of cytosines are methylated as part of CpG dinucleotides. They, in turn, form CpG islands, which are clusters of these dinucleotides. Islands located in the regulatory elements of genes are in particular interest. They are assumed to play an important role in the regulation of gene expression in humans. Besides that, cytosine methylation serves the functions of genomic imprinting, transposon suppression, epigenetic memory maintenance, X- chromosome inactivation, and embryonic development. Of particular interest are the enzymatic processes of methylation and demethylation. The methylation process always depends on the work of enzymatic complexes and is very precisely regulated. The methylation process largely depends on the functioning of three groups of enzymes: writers, readers and erasers. Writers include proteins of the DNMT family, readers are proteins containing the MBD, BTB/POZ or SET- and RING-associated domains and erasers are proteins of the TET family. Whereas demethylation can be performed not only by enzymatic complexes, but also passively during DNA replication. Hence, the maintenance of DNA methylation is important. Changes in methylation patterns are observed during embryonic development, aging, and cancers. In both aging and cancer, massive hypomethylation of the genome with local hypermethylation is observed. In this review, we will review the current understanding of the mechanisms of DNA methylation and demethylation in humans, the structure and distribution of CpG islands, the role of methylation in the regulation of gene expression, embryogenesis, aging, and cancer development.
Collapse
Affiliation(s)
- A Sergeeva
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - K Davydova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - A Perenkov
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| | - M Vedunova
- Institute of Biology and Biomedicine, National Research Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, 603022, Russia
| |
Collapse
|
12
|
Li Y, Lu X, Yu Z, Wang H, Gao B. Meta-data analysis of kidney stone disease highlights ATP1A1 involvement in renal crystal formation. Redox Biol 2023; 61:102648. [PMID: 36871182 PMCID: PMC10009205 DOI: 10.1016/j.redox.2023.102648] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/11/2023] [Accepted: 02/25/2023] [Indexed: 03/02/2023] Open
Abstract
Nephrolithiasis is a complicated disease affected by various environmental and genetic factors. Crystal-cell adhesion is a critical initiation process during kidney stone formation. However, genes regulated by environmental and genetic factors in this process remain unclear. In the present study, we integrated the gene expression profile data and the whole-exome sequencing data of patients with calcium stones, and found that ATP1A1 might be a key susceptibility gene involved in calcium stone formation. The study showed that the T-allele of rs11540947 in the 5'-untranslated region of ATP1A1 was associated with a higher risk of nephrolithiasis and lower activity of a promoter of ATP1A1. Calcium oxalate crystal deposition decreased ATP1A1 expression in vitro and in vivo and was accompanied by the activation of the ATP1A1/Src/ROS/p38/JNK/NF-κB signaling pathway. However, the overexpression of ATP1A1 or treatment with pNaKtide, a specific inhibitor of the ATP1A1/Src complex, inhibited the ATP1A1/Src signal system and alleviated oxidative stress, inflammatory responses, apoptosis, crystal-cell adhesion, and stone formation. Moreover, the DNA methyltransferase inhibitor 5-aza-2'-deoxycytidine reversed ATP1A1 down-regulation induced by crystal deposition. In conclusion, this is the first study to show that ATP1A1, a gene modulated by environmental factors and genetic variations, plays an important role in renal crystal formation, suggesting that ATP1A1 may be a potential therapeutic target for treating calcium stones.
Collapse
Affiliation(s)
- Yang Li
- Department of Biochemistry and Molecular Biology, Life Science School, Liaoning University, Shenyang, 110036, China; Department of Cell biology and Genetics, Shenyang Medical College, Shenyang 110034, China
| | - Xiuli Lu
- Department of Biochemistry and Molecular Biology, Life Science School, Liaoning University, Shenyang, 110036, China
| | - Zhihao Yu
- Department of Cell biology and Genetics, Shenyang Medical College, Shenyang 110034, China
| | - Haozhen Wang
- Department of Biochemistry and Molecular Biology, Life Science School, Liaoning University, Shenyang, 110036, China
| | - Bing Gao
- Department of Cell biology and Genetics, Shenyang Medical College, Shenyang 110034, China.
| |
Collapse
|
13
|
Sinha D, Datta S, Mishra R, Agarwal P, Kumari T, Adeyemi SB, Kumar Maurya A, Ganguly S, Atique U, Seal S, Kumari Gupta L, Chowdhury S, Chen JT. Negative Impacts of Arsenic on Plants and Mitigation Strategies. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091815. [PMID: 37176873 PMCID: PMC10181087 DOI: 10.3390/plants12091815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/21/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Arsenic (As) is a metalloid prevalent mainly in soil and water. The presence of As above permissible levels becomes toxic and detrimental to living organisms, therefore, making it a significant global concern. Humans can absorb As through drinking polluted water and consuming As-contaminated food material grown in soil having As problems. Since human beings are mobile organisms, they can use clean uncontaminated water and food found through various channels or switch from an As-contaminated area to a clean area; but plants are sessile and obtain As along with essential minerals and water through roots that make them more susceptible to arsenic poisoning and consequent stress. Arsenic and phosphorus have many similarities in terms of their physical and chemical characteristics, and they commonly compete to cause physiological anomalies in biological systems that contribute to further stress. Initial indicators of arsenic's propensity to induce toxicity in plants are a decrease in yield and a loss in plant biomass. This is accompanied by considerable physiological alterations; including instant oxidative surge; followed by essential biomolecule oxidation. These variables ultimately result in cell permeability and an electrolyte imbalance. In addition, arsenic disturbs the nucleic acids, the transcription process, and the essential enzymes engaged with the plant system's primary metabolic pathways. To lessen As absorption by plants, a variety of mitigation strategies have been proposed which include agronomic practices, plant breeding, genetic manipulation, computer-aided modeling, biochemical techniques, and the altering of human approaches regarding consumption and pollution, and in these ways, increased awareness may be generated. These mitigation strategies will further help in ensuring good health, food security, and environmental sustainability. This article summarises the nature of the impact of arsenic on plants, the physio-biochemical mechanisms evolved to cope with As stress, and the mitigation measures that can be employed to eliminate the negative effects of As.
Collapse
Affiliation(s)
- Dwaipayan Sinha
- Department of Botany, Government General Degree College, Mohanpur 721436, Paschim Medinipur, West Bengal, India
| | - Soumi Datta
- Bioactive Natural Product Laboratory, School of Interdisciplinary Sciences and Technology, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India
| | - Reema Mishra
- Department of Botany, Gargi College, University of Delhi, New Delhi 110049, India
| | - Preeti Agarwal
- Department of Botany, Gargi College, University of Delhi, New Delhi 110049, India
| | - Tripti Kumari
- Department of Chemistry, Gargi College, University of Delhi, New Delhi 110049, India
| | - Sherif Babatunde Adeyemi
- Ethnobotany/Phytomedicine Laboratory, Department of Plant Biology, Faculty of Life Sciences, University of Ilorin, Ilorin PMB 1515, Kwara State, Nigeria
| | - Arun Kumar Maurya
- Department of Botany, Multanimal Modi College, Modinagar, Ghaziabad 201204, Uttar Pradesh, India
| | - Sharmistha Ganguly
- University Department of Botany, Ranchi University, Ranchi 834008, Jharkhand, India
| | - Usman Atique
- Department of Bioscience and Biotechnology, College of Biological Systems, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Sanchita Seal
- Department of Botany, Polba Mahavidyalaya, Polba 712148, West Bengal, India
| | - Laxmi Kumari Gupta
- Bioprocess Development Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Shahana Chowdhury
- Department of Biotechnology, Faculty of Engineering Sciences, German University Bangladesh, TNT Road, Telipara, Chandona Chowrasta, Gazipur 1702, Bangladesh
| | - Jen-Tsung Chen
- Department of Life Sciences, National University of Kaohsiung, Kaohsiung 811, Taiwan
| |
Collapse
|
14
|
Castro-Muñoz LJ, Vázquez Ulloa E, Sahlgren C, Lizano M, De La Cruz-Hernández E, Contreras-Paredes A. Modulating epigenetic modifications for cancer therapy (Review). Oncol Rep 2023; 49:59. [PMID: 36799181 PMCID: PMC9942256 DOI: 10.3892/or.2023.8496] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 11/08/2022] [Indexed: 02/12/2023] Open
Abstract
Cancer is a global public health concern. Alterations in epigenetic processes are among the earliest genomic aberrations occurring during cancer development and are closely related to progression. Unlike genetic mutations, aberrations in epigenetic processes are reversible, which opens the possibility for novel pharmacological treatments. Non‑coding RNAs (ncRNAs) represent an essential epigenetic mechanism, and emerging evidence links ncRNAs to carcinogenesis. Epigenetic drugs (epidrugs) are a group of promising target therapies for cancer treatment acting as coadjuvants to reverse drug resistance in cancer. The present review describes central epigenetic aberrations during malignant transformation and explains how epidrugs target DNA methylation, histone modifications and ncRNAs. Furthermore, clinical trials focused on evaluating the effect of these epidrugs alone or in combination with other anticancer therapies and other ncRNA‑based therapies are discussed. The use of epidrugs promises to be an effective tool for reversing drug resistance in some patients with cancer.
Collapse
Affiliation(s)
| | - Elenaé Vázquez Ulloa
- Faculty of Science and Engineering/Cell Biology, University of Turku and Åbo Akademi University, Turku 20500, Finland,Turku Bioscience, University of Turku and Åbo Akademi University, Turku 20500, Finland
| | - Cecilia Sahlgren
- Faculty of Science and Engineering/Cell Biology, University of Turku and Åbo Akademi University, Turku 20500, Finland,Turku Bioscience, University of Turku and Åbo Akademi University, Turku 20500, Finland,Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands,Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven 5600 MB, The Netherlands
| | - Marcela Lizano
- Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Ciudad de Mexico 14080, Mexico,Departamento de Medicina Genomica y Toxicologia Ambiental, Instituto de Investigaciones Biomedicas, Universidad Nacional Autonoma de Mexico, Mexico 04510, Mexico
| | - Erick De La Cruz-Hernández
- Laboratory of Research in Metabolic and Infectious Diseases, Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco, Tabasco 86650, Mexico
| | - Adriana Contreras-Paredes
- Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Ciudad de Mexico 14080, Mexico,Correspondence to: Professor Adriana Contreras-Paredes, Unidad de Investigacion Biomedica en Cancer, Instituto Nacional de Cancerología-Universidad Nacional Autonoma de Mexico, Avenue San Fernando, Col. Sección XVI, Tlalpan, Ciudad de Mexico 14080, Mexico, E-mail:
| |
Collapse
|
15
|
Targeting emerging cancer hallmarks by transition metal complexes: Epigenetic reprogramming and epitherapies. Part II. Coord Chem Rev 2023. [DOI: 10.1016/j.ccr.2022.214899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
16
|
Sui JSY, Martin P, Keogh A, Murchan P, Ryan L, Nicholson S, Cuffe S, Broin PÓ, Finn SP, Fitzmaurice GJ, Ryan R, Young V, Gray SG. Altered expression of ACOX2 in non-small cell lung cancer. BMC Pulm Med 2022; 22:321. [PMID: 35999530 PMCID: PMC9396774 DOI: 10.1186/s12890-022-02115-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/16/2022] [Indexed: 12/24/2022] Open
Abstract
Peroxisomes are organelles that play essential roles in many metabolic processes, but also play roles in innate immunity, signal transduction, aging and cancer. One of the main functions of peroxisomes is the processing of very-long chain fatty acids into metabolites that can be directed to the mitochondria. One key family of enzymes in this process are the peroxisomal acyl-CoA oxidases (ACOX1, ACOX2 and ACOX3), the expression of which has been shown to be dysregulated in some cancers. Very little is however known about the expression of this family of oxidases in non-small cell lung cancer (NSCLC). ACOX2 has however been suggested to be elevated at the mRNA level in over 10% of NSCLC, and in the present study using both standard and bioinformatics approaches we show that expression of ACOX2 is significantly altered in NSCLC. ACOX2 mRNA expression is linked to a number of mutated genes, and associations between ACOX2 expression and tumour mutational burden and immune cell infiltration were explored. Links between ACOX2 expression and candidate therapies for oncogenic driver mutations such as KRAS were also identified. Furthermore, levels of acyl-CoA oxidases and other associated peroxisomal genes were explored to identify further links between the peroxisomal pathway and NSCLC. The results of this biomarker driven study suggest that ACOX2 may have potential clinical utility in the diagnosis, prognosis and stratification of patients into various therapeutically targetable options.
Collapse
Affiliation(s)
- Jane S Y Sui
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland.,Department of Medicine, Thoracic Oncology Service, Memorial Sloan Kettering Cancer Center, New York, USA
| | - Petra Martin
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland.,Midland Regional Hospital Tullamore, Tullamore, Ireland
| | - Anna Keogh
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland
| | - Pierre Murchan
- Department of Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland.,School of Mathematics, Statistics, and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Lisa Ryan
- Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - Siobhan Nicholson
- Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - Sinead Cuffe
- HOPE Directorate, St James's Hospital, Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematics, Statistics, and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - Stephen P Finn
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland.,Department of Histopathology and Morbid Anatomy, Trinity College Dublin, Dublin, Ireland.,Department of Histopathology, Labmed Directorate, St. James's Hospital, Dublin, Ireland.,Cancer Molecular Diagnostics, Labmed Directorate, St. James's Hospital, Dublin, Ireland
| | - Gerard J Fitzmaurice
- Surgery, Anaesthesia and Critical Care Directorate, St James's Hospital, Dublin, Ireland
| | - Ronan Ryan
- Surgery, Anaesthesia and Critical Care Directorate, St James's Hospital, Dublin, Ireland
| | - Vincent Young
- Surgery, Anaesthesia and Critical Care Directorate, St James's Hospital, Dublin, Ireland
| | - Steven G Gray
- Thoracic Oncology Research Group, Laboratory Medicine and Molecular Pathology, Central Pathology Laboratory, St. James's Hospital, Dublin, D08RX0X, Ireland. .,Department of Clinical Medicine, Trinity College Dublin, Dublin, Ireland. .,School of Biological Sciences, Technological University Dublin, Dublin, Ireland.
| |
Collapse
|
17
|
Hu S, Molina L, Tao J, Liu S, Hassan M, Singh S, Poddar M, Bell A, Sia D, Oertel M, Raeman R, Nejak-Bowen K, Singhi A, Luo J, Monga SP, Ko S. NOTCH-YAP1/TEAD-DNMT1 Axis Drives Hepatocyte Reprogramming Into Intrahepatic Cholangiocarcinoma. Gastroenterology 2022; 163:449-465. [PMID: 35550144 PMCID: PMC9329208 DOI: 10.1053/j.gastro.2022.05.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/15/2022] [Accepted: 05/02/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Intrahepatic cholangiocarcinoma (ICC) is a devastating liver cancer with extremely high intra- and inter-tumoral molecular heterogeneity, partly due to its diverse cellular origins. We investigated clinical relevance and the molecular mechanisms underlying hepatocyte (HC)-driven ICC development. METHODS Expression of ICC driver genes in human diseased livers at risk for ICC development were examined. The sleeping beauty and hydrodynamic tail vein injection based Akt-NICD/YAP1 ICC model was used to investigate pathogenetic roles of SRY-box transcription factor 9 (SOX9) and yes-associated protein 1 (YAP1) in HC-driven ICC. We identified DNA methyltransferase 1 (DNMT1) as a YAP1 target, which was validated by loss- and gain-of-function studies, and its mechanism addressed by chromatin immunoprecipitation sequencing. RESULTS Co-expression of AKT and Notch intracellular domain (NICD)/YAP1 in HC yielded ICC that represents 13% to 29% of clinical ICC. NICD independently regulates SOX9 and YAP1 and deletion of either, significantly delays ICC development. Yap1 or TEAD inhibition, but not Sox9 deletion, impairs HC-to-biliary epithelial cell (BEC) reprogramming. DNMT1 was discovered as a novel downstream effector of YAP1-TEAD complex that directs HC-to-BEC/ICC fate switch through the repression of HC-specific genes regulated by master regulators for HC differentiation, including hepatocyte nuclear factor 4 alpha, hepatocyte nuclear factor 1 alpha, and CCAAT/enhancer-binding protein alpha/beta. DNMT1 loss prevented NOTCH/YAP1-dependent HC-driven cholangiocarcinogenesis, and DNMT1 re-expression restored ICC development following TEAD repression. Co-expression of DNMT1 with AKT was sufficient to induce tumor development including ICC. DNMT1 was detected in a subset of HCs and dysplastic BECs in cholestatic human livers prone to ICC development. CONCLUSION We identified a novel NOTCH-YAP1/TEAD-DNMT1 axis essential for HC-to-BEC/ICC conversion, which may be relevant in cholestasis-to-ICC pathogenesis in the clinic.
Collapse
Affiliation(s)
- Shikai Hu
- School of Medicine, Tsinghua University, Beijing, China;,Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Laura Molina
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Junyan Tao
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Silvia Liu
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA;,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Mohammed Hassan
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Sucha Singh
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Minakshi Poddar
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Aaron Bell
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Daniela Sia
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Michael Oertel
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA;,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Reben Raeman
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA;,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Kari Nejak-Bowen
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA;,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Aatur Singhi
- Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, PA USA;,Division of Anatomic Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Jianhua Luo
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA;,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, PA USA
| | - Satdarshan P. Monga
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA USA;,Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, PA USA;,Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, PA USA;,Co-Corresponding Authors: Sungjin Ko, D.V.M., Ph.D., Assistant Professor, Department of Pathology and Pittsburgh Liver Research Center, University of Pittsburgh, School of Medicine, 200 Lothrop Street S-424 BST, Pittsburgh, PA 15261, Tel: 412-648-8146; Fax: (412) 648-1916; , Satdarshan P. Monga, M.D., FAASLD., Professor of Pathology and Medicine, Director, Pittsburgh Liver Research Center, UPMC Endowed Chair, Vice Chair and Division Chief of Experimental Pathology, University of Pittsburgh, School of Medicine and UPMC, 200 Lothrop Street S-422 BST, Pittsburgh, PA 15261, Tel: (412) 648-9966; Fax: (412) 648-1916;
| | - Sungjin Ko
- Division of Experimental Pathology, Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania; Pittsburgh Liver Research Center, University of Pittsburgh Medical Center and University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania.
| |
Collapse
|
18
|
Fu S, Lu Z, Ye W. TGF- β1 Induces Interlukin-11 Expression and Pro-Fibrotic Effect by DNA Demethylation in Subconjunctival Fibroblasts. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE : ECAM 2022; 2022:7729827. [PMID: 35865343 PMCID: PMC9296281 DOI: 10.1155/2022/7729827] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 11/28/2022]
Abstract
Objective To assess Interlukin-11 (IL11) expression in the tears of patients after filtration surgery and to find out its pro-transdifferentiational and pro-fibrotic functions and mechanisms on subconjunctival human Tenon's capsule fibroblasts (HTFs) induced by transforming growth factor beta1 (TGF-β1). Methods Tears were collected from glaucoma patients with or without filtration surgery. The expression of IL11 in tears was examined by enzyme-linked immunosorbent assay. Primary HTFs were prepared as an expansion culture of human Tenon's explants from patients undergoing cataract surgery. TGF-β1 and IL11 were used to stimulate the cultured HTFs. Quantitative RT-PCR and western blot analyzed the roles of TGF-β1 in IL11 and DNA methyltransferase (DNMT) expression and the effects of IL11 on collagen-1A1 and α-smooth muscle actin expression. The effects of IL11 on human HTFs' migration were tested via the scratch-wound assay. MassARRAY platform of Sequenom was applied for analyzing the quantitative methylation of the IL11 promoter region. Result Our data presented significantly high levels of IL11 in the tears of patients who underwent filtration surgery with uncontrolled intraocular pressure (IOP) compared with those who underwent filtration surgery with controlled IOP. The up-regulation of IL11 was related to TGF-β1. We also found that TGF-β induced IL11 up-regulation in the HTFs, which activates the HTFs and enhanced the translation of the pro-fibrotic protein expression. This is correlated with inhibiting the activity and expression of DNMTs and demethylating the IL11 promoter. Therefore, IL11 may be an ideal target to be regulated to control the filtering pathway scar formation.
Collapse
Affiliation(s)
- Shuhao Fu
- Department of Ophthalmology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Zhaozeng Lu
- Department of Ophthalmology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Wen Ye
- Department of Ophthalmology, Huashan Hospital, Fudan University, Shanghai 200040, China
| |
Collapse
|
19
|
Zhao Q, Ge Z, Fu S, Wan S, Shi J, Wu Y, Zhang Y. DNA methylation plays an important role in iron-overloaded Tibetans. Gene 2022; 97:55-66. [PMID: 35644542 DOI: 10.1266/ggs.21-00006] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The prevalence of iron overload in Tibetans in Tibet is higher than that in Han. DNA methylation (DNAm) is closely related to iron metabolism and iron level. Nevertheless, the epigenetic status of Tibetans with iron overload is unknown, and we therefore aimed to explore whether the phenomenon observed in the Tibetan population is regulated by epigenetics. The results showed that 2.26% of cytosine was methylated in the whole genome, and that the rate of CG cytosine methylation was higher in individuals in the iron overload (TH) group than in those in the iron normal (TL) group. We analyzed differentially methylated genes (DMGs) in whole-genome bisulfite sequencing data from the TH and TL groups of high-altitude Tibetans. Protein-protein interaction and pathway analyses of candidate DMGs related to iron uptake and transport showed that epigenetic changes in 10 candidate genes (ACO1, CYBRD1, FLVCR1, HFE, HMOX2, IREB2, NEDD8, SLC11A2, SLC40A1 and TFRC) are likely to relate to iron overload. This work reveals, for the first time, changes of DNAm in Tibetan people with iron overload, which suggest that DNAm is a mechanism underlying differences in iron content between individuals in the high-altitude Tibetan population. Our findings should contribute to the study of iron metabolism and the overall health status of Tibetans.
Collapse
Affiliation(s)
- Qin Zhao
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital C.T.)
| | - Zhijing Ge
- School of Basic Medical Sciences, Tibet University
| | - Suhong Fu
- Laboratory of Natural Medicine, West China Hospital, West China Medical School, Sichuan University
| | - Sha Wan
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital C.T.)
| | - Jing Shi
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital C.T.)
| | - Yunhong Wu
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital C.T.)
| | - Yongqun Zhang
- Hospital of Chengdu Office of People's Government of Tibetan Autonomous Region (Hospital C.T.)
| |
Collapse
|
20
|
Salah N, Salem L, Taha S, Youssef M, Annaka L, Hassan S, Mahmoud R. DNMT3A and TET2; Potential Estimates of Generic DNA Methylation in Children and Adolescents with Obesity; Relation to Metabolic Dysregulation. Horm Res Paediatr 2022; 95:25-34. [PMID: 35066499 DOI: 10.1159/000521701] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 12/24/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION The role of DNA methylation in metabolic dysregulation is emerging. However, the functional role of methylation in obesity and metabolic dysregulation is poorly understood. AIM The aim of this study was to compare DNA methyltransferase-3A (DNMT3A) and ten-eleven translocase-2 (TET2) levels in children and adolescents with obesity to normal-weighed children and adolescents and to correlate them to various metabolic parameters. METHODS Fifty children and adolescents with obesity were compared to 50 matched normal-weighed children and adolescents. Participants underwent assessment for anthropometric measurements, Tanner staging, acanthosis nigricans, and mean blood pressure percentile on three different occasions. TET2, DNMT3A, fasting lipids, and insulin were measured with calculation of the homeostatic model assessment insulin resistance (HOMA-IR). RESULTS The median BMI SDS of the studied children and adolescents with obesity was 3.40, their mean TET2 was 178.40 ng/mL, and their mean DNMT3A was 2.18 ng/mL. TET2 is significantly lower (p = 0.009), while DNMT3A is significantly higher (p < 0.001) in children and adolescents with obesity than controls. Children and adolescents with obesity and insulin resistance have significantly lower TET2 (p = 0.012) and significantly higher DNMT3A (p = 0.013) than those without insulin resistance. Diastolic blood pressure percentile and HOMA-IR are positively correlated to DNMT3A (p < 0.001) and negatively correlated to TET-2 (p < 0.001). Multivariate logistic regression analysis revealed that TET2 and DNMT3A are independently associated with diastolic blood pressure percentile (p = 0.03 and p = 0.014, respectively) and HOMA-IR (p = 0.003 and p = 0.001, respectively). CONCLUSIONS Children and adolescents with obesity have significantly higher DNMT3A and significantly lower TET2 than controls. This is more evident in those having insulin resistance than those without. DNMT3A and TET2 are independently associated with systemic hypertension and insulin resistance in children with obesity.
Collapse
Affiliation(s)
- Nouran Salah
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Lamyaa Salem
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Sara Taha
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Mariam Youssef
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Layla Annaka
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Safeya Hassan
- Department of Clinical Pathology, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Rana Mahmoud
- Department of Pediatrics, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| |
Collapse
|
21
|
The World of Oral Cancer and Its Risk Factors Viewed from the Aspect of MicroRNA Expression Patterns. Genes (Basel) 2022; 13:genes13040594. [PMID: 35456400 PMCID: PMC9027895 DOI: 10.3390/genes13040594] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 01/27/2023] Open
Abstract
Oral cancer is one of the leading causes of death worldwide, with a reported 5-year survival rate of around 50% after treatment. Epigenetic modifications are considered to have a key role in oral carcinogenesis due to histone modifications, aberrant DNA methylation, and altered expression of miRNAs. MicroRNAs (miRNAs) are small non-coding RNAs that have a key role in cancer development by regulating signaling pathways involved in carcinogenesis. MiRNA deregulation identified in oral cancer has led to the idea of using them as potential biomarkers for early diagnosis, prognosis, and the development of novel therapeutic strategies. In recent years, a key role has been observed for risk factors in preventing and treating this malignancy. The purpose of this review is to summarize the recent knowledge about the altered mechanisms of oral cancer due to risk factors and the role of miRNAs in these mechanisms.
Collapse
|
22
|
Shi Y, Huang R, Zhang Y, Feng Q, Pan X, Wang L. RNA Interference Induces BRCA1 Gene Methylation and Increases the Radiosensitivity of Breast Cancer Cells. Cancer Biother Radiopharm 2022. [PMID: 35180362 DOI: 10.1089/cbr.2021.0346] [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: 11/12/2022] Open
Abstract
Purpose: To investigate the relationship between breast cancer susceptibility gene-1 (BRCA1) gene methylation and the radiosensitivity of breast cancer. Materials and Methods: The authors studied three breast cancer cell lines: MDA-MB-435, MDA-MB-231, and MCF-7 cells. They constructed five short hairpin RNAs (shRNAs) and five small interfering RNAs to target selected promoter loci and initiate sequence-specific methylation in breast cancer cells. Pyrosequencing was used to analyze the state of DNA methylation. Quantitative real-time polymerase chain reaction was used to detect BRCA1 mRNA expression and RNA-directed DNA methylation (RdDM)-related gene expression. Western blotting was performed to analyze BRCA1 protein expression. Colony formation assays and γ-histone H2A foci formation assays were conducted to assess the surviving fraction (SF) and double-strand break (DSB) repair ability of cells after irradiation. Results: The authors constructed five strains of lentivirus vectors and five plasmid vectors targeting BRCA1 promoter region. In MDA-MB-435 cells, lentivirus-mediated RNA interference targeting Site 1 of BRCA1 increased the methylation levels of BRCA1 and reduced BRCA1 mRNA and protein expression. The SF and the ability to repair DNA DSBs were reduced in the combined LV-BRCA1RNAi-Site 1 infection and irradiation group. Conclusions: The authors' findings suggest that the shRNA suppressed the expression levels of the BRCA1 gene and reduced the SF and DNA repair ability of cells after irradiation through RdDM. In summary, the radiosensitivity of breast cancer cells may correlate with BRCA1 methylation. Advances in Knowledge: The authors first utilized a lentivirus-based shRNA-mediated specific-sequence DNA methylation of the BRCA1 gene mediated by RdDM.
Collapse
Affiliation(s)
- Yuebin Shi
- Department of Pathology, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| | - Rui Huang
- Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yong Zhang
- Department of Radiation Oncology, The First Affiliated Hospital of Kunming Medical University, Kunming, Yunnan, China
| | - Qiang Feng
- Department of Pathology, 920th Hospital of Joint Logistics Support Force of PLA, Kunming, Yunnan, China
| | - Xinyan Pan
- Department of Pathology, 920th Hospital of Joint Logistics Support Force of PLA, Kunming, Yunnan, China
| | - Li Wang
- Department of Pathology, The First People's Hospital of Yunnan Province, Kunming, Yunnan, China
| |
Collapse
|
23
|
Long Noncoding RNAs Regulate the Radioresistance of Breast Cancer. Anal Cell Pathol (Amst) 2021; 2021:9005073. [PMID: 34595090 PMCID: PMC8478560 DOI: 10.1155/2021/9005073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/10/2021] [Accepted: 08/19/2021] [Indexed: 12/15/2022] Open
Abstract
Breast cancer (BRCA) has severely threatened women's health worldwide. Radiotherapy is a treatment for BRCA, which applies high doses of ionizing radiation to induce cancer cell death and reduce disease recurrence. Radioresistance is one of the most important elements that affect the therapeutic efficacy of radiotherapy. Long noncoding RNAs (lncRNAs) are suggested to dominate crucial roles in regulating the biological behavior of BRCA. Currently, some studies indicate that overexpression or inhibition of lncRNAs can greatly alter the radioresistance of BRCA. In this review, we summarized the knowledge on the classification and function of lncRNAs and the molecular mechanism of BRCA radioresistance, listed lncRNAs related to the BRCA radioresistance, highlighted their underlying mechanisms, and discussed the potential application of these lncRNAs in regulating BRCA radioresistance.
Collapse
|
24
|
Kaplun D, Starshin A, Sharko F, Gainova K, Filonova G, Zhigalova N, Mazur A, Prokhortchouk E, Zhenilo S. Kaiso Regulates DNA Methylation Homeostasis. Int J Mol Sci 2021; 22:7587. [PMID: 34299205 PMCID: PMC8307659 DOI: 10.3390/ijms22147587] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/09/2021] [Accepted: 07/13/2021] [Indexed: 01/31/2023] Open
Abstract
Gain and loss of DNA methylation in cells is a dynamic process that tends to achieve an equilibrium. Many factors are involved in maintaining the balance between DNA methylation and demethylation. Previously, it was shown that methyl-DNA protein Kaiso may attract NCoR, SMRT repressive complexes affecting histone modifications. On the other hand, the deficiency of Kaiso resulted in reduced methylation of ICR in H19/Igf2 locus and Oct4 promoter in mouse embryonic fibroblasts. However, nothing is known about how Kaiso influences DNA methylation at the genome level. Here we show that deficiency of Kaiso led to whole-genome hypermethylation, using Kaiso deficient human renal cancer cell line obtained via CRISPR/CAS9 genome editing. However, Kaiso serves to protect genic regions, enhancers, and regions with a low level of histone modifications from demethylation. We detected hypomethylation of binding sites for Oct4 and Nanog in Kaiso deficient cells. Kaiso immunoprecipitated with de novo DNA methyltransferases DNMT3a/3b, but not with maintenance methyltransferase DNMT1. Thus, Kaiso may attract methyltransferases to surrounding regions and modulate genome methylation in renal cancer cells apart from being methyl DNA binding protein.
Collapse
Affiliation(s)
- Darya Kaplun
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia; (D.K.); (A.S.); (F.S.); (G.F.); (N.Z.); (A.M.)
- Institute of Gene Biology RAS, 119071 Moscow, Russia
| | - Alexey Starshin
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia; (D.K.); (A.S.); (F.S.); (G.F.); (N.Z.); (A.M.)
| | - Fedor Sharko
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia; (D.K.); (A.S.); (F.S.); (G.F.); (N.Z.); (A.M.)
| | - Kristina Gainova
- Centre for Strategic Planning of FMBA of Russia, 119071 Moscow, Russia;
| | - Galina Filonova
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia; (D.K.); (A.S.); (F.S.); (G.F.); (N.Z.); (A.M.)
| | - Nadezhda Zhigalova
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia; (D.K.); (A.S.); (F.S.); (G.F.); (N.Z.); (A.M.)
| | - Alexander Mazur
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia; (D.K.); (A.S.); (F.S.); (G.F.); (N.Z.); (A.M.)
- Institute of Gene Biology RAS, 119071 Moscow, Russia
| | - Egor Prokhortchouk
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia; (D.K.); (A.S.); (F.S.); (G.F.); (N.Z.); (A.M.)
- Institute of Gene Biology RAS, 119071 Moscow, Russia
| | - Svetlana Zhenilo
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia; (D.K.); (A.S.); (F.S.); (G.F.); (N.Z.); (A.M.)
- Institute of Gene Biology RAS, 119071 Moscow, Russia
| |
Collapse
|
25
|
Kobayashi M, Deguchi Y, Nozaki Y, Higami Y. Contribution of PGC-1α to Obesity- and Caloric Restriction-Related Physiological Changes in White Adipose Tissue. Int J Mol Sci 2021; 22:ijms22116025. [PMID: 34199596 PMCID: PMC8199692 DOI: 10.3390/ijms22116025] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/28/2021] [Accepted: 05/31/2021] [Indexed: 12/16/2022] Open
Abstract
Peroxisome proliferator-activated receptor γ coactivator-1 α (PGC-1α) regulates mitochondrial DNA replication and mitochondrial gene expression by interacting with several transcription factors. White adipose tissue (WAT) mainly comprises adipocytes that store triglycerides as an energy resource and secrete adipokines. The characteristics of WAT vary in response to systemic and chronic metabolic alterations, including obesity or caloric restriction. Despite a small amount of mitochondria in white adipocytes, accumulated evidence suggests that mitochondria are strongly related to adipocyte-specific functions, such as adipogenesis and lipogenesis, as well as oxidative metabolism for energy supply. Therefore, PGC-1α is expected to play an important role in WAT. In this review, we provide an overview of the involvement of mitochondria and PGC-1α with obesity- and caloric restriction-related physiological changes in adipocytes and WAT.
Collapse
Affiliation(s)
- Masaki Kobayashi
- Laboratory of Molecular Pathology and Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan; (Y.D.); (Y.N.)
- Correspondence: (M.K.); (Y.H.); Tel.: +81-4-7121-3676 (M.K. & Y.H.)
| | - Yusuke Deguchi
- Laboratory of Molecular Pathology and Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan; (Y.D.); (Y.N.)
| | - Yuka Nozaki
- Laboratory of Molecular Pathology and Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan; (Y.D.); (Y.N.)
| | - Yoshikazu Higami
- Laboratory of Molecular Pathology and Metabolic Disease, Faculty of Pharmaceutical Sciences, Tokyo University of Science, 2641 Yamazaki, Noda 278-8510, Japan; (Y.D.); (Y.N.)
- Research Institute for Biomedical Sciences, Tokyo University of Science, 2669 Yamazaki, Noda 278-8510, Japan
- Correspondence: (M.K.); (Y.H.); Tel.: +81-4-7121-3676 (M.K. & Y.H.)
| |
Collapse
|
26
|
De Dieuleveult M, Bizet M, Colin L, Calonne E, Bachman M, Li C, Stancheva I, Miotto B, Fuks F, Deplus R. The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome. Epigenetics 2021; 17:422-443. [PMID: 33960278 DOI: 10.1080/15592294.2021.1917152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ten-Eleven Translocation (TET) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) leading to a dynamic epigenetic state of DNA that can influence transcription and chromatin organization. While TET proteins interact with complexes involved in transcriptional repression and activation, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene expression still remains limited. Here, we show that TET proteins interact with the chromatin remodelling protein lymphoid-specific helicase (LSH/HELLS) in vivo and in vitro. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESCs) knock out of Lsh leads to a significant reduction of 5-hydroxymethylation amount in the DNA. Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh, some regions of the genome gain 5hmC while others lose it, with mild correlation with gene expression changes. We further show that differentially hydroxymethylated regions did not completely overlap with differentially methylated regions indicating that changes in 5hmC distribution upon Lsh knock-out are not a direct consequence of 5mC decrease. Altogether, our results suggest that LSH, which interacts with TET proteins, contributes to the regulation of 5hmC levels and distribution in MEFs and ESCs.
Collapse
Affiliation(s)
- Maud De Dieuleveult
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium.,Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Laurence Colin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Martin Bachman
- Medicines Discovery Catapult, Alderley Park, Macclesfield, UK
| | - Chao Li
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Irina Stancheva
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Benoit Miotto
- Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| |
Collapse
|