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Zheng P, Raj P, Liang L, Wu L, Paidi SK, Kim JH, Barman I. Label-free plasmonic spectral profiling of serum DNA. Biosens Bioelectron 2024; 254:116199. [PMID: 38492362 DOI: 10.1016/j.bios.2024.116199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/07/2024] [Accepted: 03/07/2024] [Indexed: 03/18/2024]
Abstract
Genetic and epigenetic modifications are linked to the activation of oncogenes and inactivation of tumor suppressor genes. Likewise, the associated molecular alternations can best inform precision medicine for personalized tumor treatment. Therefore, performing characterization of genetic and epigenetic alternations at the molecular level represents a crucial step in early diagnosis and/or therapeutics of cancer. However, the prevailing methods for DNA analysis involve a series of tedious and complicated steps, in which important genetic and epigenetic information could be lost or altered. To provide a potential approach for non-invasive, direct, and efficient DNA analysis, herein, we present a promising strategy for label-free molecular profiling of serum DNA in its pristine form by fusing surface-enhanced Raman spectroscopy with machine learning on a superior plasmonic nanostructured platform. Using DNA methylation and single-point mutation as two case studies, the presented strategy allows a well-balanced sensitive and specific detection of epigenetic and genetic changes at the single-nucleotide level in serum. We envision the presented label-free strategy could serve as a versatile tool for direct molecular profiling in pristine forms of a wide range of biological markers and aid biomedical diagnostics as well as therapeutics.
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Affiliation(s)
- Peng Zheng
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Piyush Raj
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Le Liang
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States; The Institute for Advanced Studies, Wuhan University, Wuhan, 430072, China; Department of Ophthalmology, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, 430071, China
| | - Lintong Wu
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Santosh Kumar Paidi
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Jeong Hee Kim
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States
| | - Ishan Barman
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, MD, 21218, United States; Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, United States; The Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, United States.
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Alexander WB, Wang W, Hill MA, O'Dell MR, Ruffolo LI, Guo B, Jackson KM, Ullman N, Friedland SC, McCall MN, Patel A, Figueroa-Guilliani N, Georger M, Belt BA, Whitney-Miller CL, Linehan DC, Murphy PJ, Hezel AF. Smad4 restricts injury-provoked biliary proliferation and carcinogenesis. Dis Model Mech 2024; 17:dmm050358. [PMID: 38415925 PMCID: PMC10924230 DOI: 10.1242/dmm.050358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/10/2023] [Indexed: 02/29/2024] Open
Abstract
Cholangiocarcinoma (CCA) is a deadly and heterogeneous type of cancer characterized by a spectrum of epidemiologic associations as well as genetic and epigenetic alterations. We seek to understand how these features inter-relate in the earliest phase of cancer development and through the course of disease progression. For this, we studied murine models of liver injury integrating the most commonly occurring gene mutations of CCA - including Kras, Tp53, Arid1a and Smad4 - as well as murine hepatobiliary cancer models and derived primary cell lines based on these mutations. Among commonly mutated genes in CCA, we found that Smad4 functions uniquely to restrict reactive cholangiocyte expansion to liver injury through restraint of the proliferative response. Inactivation of Smad4 accelerates carcinogenesis, provoking pre-neoplastic biliary lesions and CCA development in an injury setting. Expression analyses of Smad4-perturbed reactive cholangiocytes and CCA lines demonstrated shared enriched pathways, including cell-cycle regulation, MYC signaling and oxidative phosphorylation, suggesting that Smad4 may act via these mechanisms to regulate cholangiocyte proliferation and progression to CCA. Overall, we showed that TGFβ/SMAD4 signaling serves as a critical barrier restraining cholangiocyte expansion and malignant transformation in states of biliary injury.
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Affiliation(s)
- William B. Alexander
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Wenjia Wang
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Margaret A. Hill
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Michael R. O'Dell
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Luis I. Ruffolo
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Bing Guo
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Katherine M. Jackson
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Nicholas Ullman
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Scott C. Friedland
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Matthew N. McCall
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ankit Patel
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | | | - Mary Georger
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Brian A. Belt
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Christa L. Whitney-Miller
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - David C. Linehan
- Department of Surgery, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Patrick J. Murphy
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Aram F. Hezel
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, NY 14642, USA
- Department of Medicine, Hematology/Oncology, Wilmot Cancer Institute, University of Rochester Medical Center, Rochester, NY 14642, USA
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Kang HJ, Kim JW, Kim JT, Park MS, Chun BJ, Kim SW, Shin IS, Stewart R, Kim JM. Brain Derived Neurotrophic Factor Methylation and Long-term Outcomes after Stroke Interacting with Suicidal Ideation. Clin Psychopharmacol Neurosci 2024; 22:306-313. [PMID: 38627077 DOI: 10.9758/cpn.23.1115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 04/20/2024]
Abstract
Objective This study aimed to evaluate the unexplored relationship between BDNF methylation, long-term outcomes, and its interaction with suicidal ideation (SI), which is closely associated with both BDNF expression and stroke outcomes. Methods A total of 278 stroke patients were assessed for BDNF methylation status and SI using suicide-related item in the Montgomery-Åsberg Depression Rating Scale at 2 weeks post-stroke. We investigated the incidence of composite cerebro-cardiovascular events (CCVEs) during an 8-14-year period after the initial stroke as long-term stroke outcome. We conducted Cox regression models adjusted for covariates to evaluate the association between BDNF methylation status and CCVEs, as well as its interaction with post-stroke SI at 2 weeks. Results Higher methylation status of CpG 1, 3, and 5, but not the average value, predicted a greater number of composite CCVEs during 8-14 years following the stroke. The associations between a higher methylation status of CpGs 1, 3, 5, and 8, as well as the average BDNF methylation value, and a greater number of composite CCVEs, were prominent in patients who had post-stroke SI at 2 weeks. Notably, a significant interaction between methylation status and SI on composite CCVEs was observed only for CpG 8. Conclusion The significant association between BDNF methylation and poor long-term stroke outcomes, particularly amplified in individuals who had post-stroke SI at 2 weeks, suggested that evaluating the biological marker status of BDNF methylation along with assessing SI during the acute phase of stroke can help predict long-term outcomes.
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Affiliation(s)
- Hee-Ju Kang
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
| | - Ju-Wan Kim
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
| | - Joon-Tae Kim
- Department of Neurology, Chonnam National University Medical School, Gwangju, Korea
| | - Man-Seok Park
- Department of Neurology, Chonnam National University Medical School, Gwangju, Korea
| | - Byung Jo Chun
- Department of Emergency Medicine, Chonnam National University Medical School, Gwangju, Korea
| | - Sung-Wan Kim
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
| | - Il-Seon Shin
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
| | - Robert Stewart
- King's College London (Institute of Psychiatry, Psychology and Neuroscience), London, UK
- South London and Maudsley NHS Foundation Trust, London, UK
| | - Jae-Min Kim
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
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Ishidoya M, Fujita T, Tasaka S, Fujii H. Real-time MBDi-RPA using methyl-CpG binding protein 2: A real-time detection method for simple and rapid estimation of CpG methylation status. Anal Chim Acta 2024; 1302:342486. [PMID: 38580404 DOI: 10.1016/j.aca.2024.342486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/21/2024] [Accepted: 03/14/2024] [Indexed: 04/07/2024]
Abstract
BACKGROUND Analysis of CpG methylation is informative for cancer diagnosis. Previously, we developed a novel method to discriminate CpG methylation status in target DNA by blocking recombinase polymerase amplification (RPA), an isothermal DNA amplification technique, using methyl-CpG binding domain (MBD) protein 2 (MBD2). The method was named MBD protein interference-RPA (MBDi-RPA). In this study, MBDi-RPA was performed using methyl-CpG binding protein 2 (MeCP2), another MBD family protein, as the blocking agent. RESULTS MBDi-RPA using MeCP2 detected low levels of CpG methylation, showing that it had higher sensitivity than MBDi-RPA using MBD2. We also developed real-time RPA, which enabled rapid analysis of DNA amplification without the need for laborious agarose gel electrophoresis and used it in combination with MBDi-RPA. We termed this method real-time MBDi-RPA. The method using MeCP2 could determine the abundance ratio of CpG-methylated target DNA simply and rapidly, although highly sensitive detection was challenging. SIGNIFICANCE AND NOVELTY Real-time MBDi-RPA using MeCP2 could be potentially useful for estimating CpG methylation status in target DNA prior to more detailed analyses.
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Affiliation(s)
- Mina Ishidoya
- Department of Respiratory Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Toshitsugu Fujita
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan.
| | - Sadatomo Tasaka
- Department of Respiratory Medicine, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
| | - Hodaka Fujii
- Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki, Aomori, 036-8562, Japan
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Tang X, Wen D, Jin X, Wang C, Xu W, Qu W, Xu R, Jia H, Liu Y, Li X, Chen S, Fu X, Liang B, Li J, Liu Y, Zha L. A preliminary study on identification of the blood donor in a body fluid mixture using a novel compound genetic marker blood-specific methylation-microhaplotype. Forensic Sci Int Genet 2024; 70:103031. [PMID: 38493735 DOI: 10.1016/j.fsigen.2024.103031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/19/2024]
Abstract
Blood-containing mixtures are frequently encountered at crime scenes involving violence and murder. However, the presence of blood, and the association of blood with a specific donor within these mixtures present significant challenges in forensic analysis. In light of these challenges, this study sought to address these issues by leveraging blood-specific methylation sites and closely linked microhaplotype sites, proposing a novel composite genetic marker known as "blood-specific methylation-microhaplotype". This marker was designed to the detection of blood and the determination of blood donor within blood-containing mixtures. According to the selection criteria mentioned in the Materials and Methods section, we selected 10 blood-specific methylation-microhaplotype loci for inclusion in this study. Among these loci, eight exhibited blood-specific hypomethylation, while the remaining two displayed blood-specific hypermethylation. Based on data obtained from 124 individual samples in our study, the combined discrimination power (CPD) of these 10 successfully sequenced loci was 0.999999298. The sample allele methylation rate (Ram) was obtained from massive parallel sequencing (MPS), which was defined as the proportion of methylated reads to the total clustered reads that were genotyped to a specific allele. To develop an allele type classification model capable of identifying the presence of blood and the blood donor, we used the Random Forest algorithm. This model was trained and evaluated using the Ram distribution of individual samples and the Ram distribution of simulated shared alleles. Subsequently, we applied the developed allele type classification model to predict alleles within actual mixtures, trying to exclude non-blood-specific alleles, ultimately allowing us to identify the presence of blood and the blood donor in the blood-containing mixtures. Our findings demonstrate that these blood-specific methylation-microhaplotype loci have the capability to not only detect the presence of blood but also accurately associate blood with the true donor in blood-containing mixtures with the mixing ratios of 1:29, 1:19, 1:9, 1:4, 1:2, 2:1, 7:1, 8:1, 31:1 and 36:1 (blood:non-blood) by DNA mixture interpretation methods. In addition, the presence of blood and the true blood donor could be identified in a mixture containing four body fluids (blood:vaginal fluid:semen:saliva = 1:1:1:1). It is important to note that while these loci exhibit great potential, the impact of allele dropouts and alleles misidentification must be considered when interpreting the results. This is a preliminary study utilising blood-specific methylation-microhaplotype as a complementary tool to other well-established genetic markers (STR, SNP, microhaplotype, etc.) for the analysis in blood-containing mixtures.
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Affiliation(s)
- Xuan Tang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Xin Jin
- Department of Public Security of Hainan Province, Haikou, Hainan Province, PR China
| | - Chudong Wang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Wei Xu
- Central Laboratory, Hunan Provincal People's Hospital (The First Affiliated Hospitak of Hunan Normal University), Changsha, Hunan Province 410000, PR China
| | - Weifeng Qu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Ruyi Xu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Hongtao Jia
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Yi Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Xue Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, Xinjiang 830017, PR China
| | - Siqi Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Xiaoyi Fu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Bin Liang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Jienan Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China
| | - Ying Liu
- Xiangya Stomatological Collage, Central South University, No72. Xiangya Road, Changsha, Hunan 410013, PR China.
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, Hunan 410013, PR China; Hebei Key Laboratory of Forensic Medicine, School of Forensic Medicine, Hebei Medical University, Shijiazhuang, PR China.
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Burdier FR, Waheed DEN, Nedjai B, Steenbergen RD, Poljak M, Baay M, Vorsters A, Van Keer S. DNA methylation as a triage tool for cervical cancer screening - A meeting report. Prev Med Rep 2024; 41:102678. [PMID: 38524273 PMCID: PMC10959704 DOI: 10.1016/j.pmedr.2024.102678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/08/2024] [Accepted: 03/05/2024] [Indexed: 03/26/2024] Open
Abstract
Introduction DNA methylation is proposed as a novel biomarker able to monitor molecular events in human papillomavirus (HPV) infection pathophysiology, enabling the distinction between HPV-induced lesions with regression potential from those that may progress to HPV-related cancer. Methods This meeting report summarises the presentations and expert discussions during the HPV Prevention and Control Board-focused topic technical meeting on DNA methylation validation in clinician-collected and self-collected samples, novel DNA methylation markers discovery, implementation in cervical cancer screening programs, and their potential in women living with human immunodeficiency virus (HIV). Results Data presented in the meeting showed that HPV-positive, baseline methylation-negative women have a lower cumulative cervical cancer incidence than baseline cytology-negative women, making DNA methylation an attractive triage strategy. However, additional standardised data in different settings (low- versus high-income settings), samples (clinician-collected and self-collected), study designs (prospective, modelling, impact) and populations (immunocompetent women, women living with HIV) are needed. Conclusion Establishing international validation guidelines were identified as the way forward towards accurate validation and subsequent implementation in current screening programs.
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Affiliation(s)
- F. Ricardo Burdier
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Belgium
| | - Dur-e-Nayab Waheed
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Belgium
| | - Belinda Nedjai
- Centre for Prevention, Diagnosis and Detection Cancer Prevention Unit, Wolfson Institute of Population Health, Queen Mary University of London, London, UK
| | - Renske D.M. Steenbergen
- Amsterdam UMC Vrije Universiteit Amsterdam, Department of Pathology, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Mario Poljak
- Institute of Immunology and Microbiology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Marc Baay
- P95 Epidemiology & Pharmacovigilance, Leuven, Belgium
| | - Alex Vorsters
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Belgium
| | - Severien Van Keer
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Belgium
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Sanwald S, Montag C, Kiefer M. Group differences in OXT methylation between patients with Major Depressive Disorder and healthy controls: A pre-registered replication study. Psychiatry Res 2024; 335:115855. [PMID: 38522151 DOI: 10.1016/j.psychres.2024.115855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/26/2024]
Abstract
Depression is linked to stress which leaves traces in the epigenetic signature of genes. The oxytocin system is implicated in allostatic processes promoting adaption to environmental stressors. Interactions of the oxytocin system with the environment, e.g., methylation of the gene coding for oxytocin (OXT), are candidates for the investigation of the biological underpinnings of depression. Recently, we found hypomethylation of OXT in patients with Major Depressive Disorder (MDD) compared to healthy controls (HC). Since the replicability of findings is a key point of criticism in (epi‑)genetic research, we aimed to confirm our previous findings in a pre-registered study (data was stored in a database prior to pre-registration) within a new sample of n = 85 patients with MDD and n = 85 HC. We investigated OXT DNA-methylation in peripheral blood samples, stressful life events and depression severity. In accordance with our previous study, we found hypomethylation of OXT in patients with MDD compared to HC. Methylation was not associated with stressful life events. Patients reported significantly more stressful life events compared to HC. Our study revealed that hypomethylation of OXT can be demonstrated in a reproducible fashion and provides further evidence for the involvement of the oxytocin system in depression.
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Affiliation(s)
- Simon Sanwald
- Ulm University, Department of Psychiatry and Psychotherapy III, Germany.
| | - Christian Montag
- Ulm University, Department of Molecular Psychology, Institute of Psychology and Education, Germany
| | - Markus Kiefer
- Ulm University, Department of Psychiatry and Psychotherapy III, Germany
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Zhou S, Cheng C, Liao YX, Wang L, Zeng JM, Zhou FF, Zhang XQ, Yang T. Epigenetic regulation of FOXI2 promotes clear cell renal cell carcinoma progression. Heliyon 2024; 10:e29218. [PMID: 38628758 PMCID: PMC11016964 DOI: 10.1016/j.heliyon.2024.e29218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 04/02/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024] Open
Abstract
In recent decades, substantial advancements in epigenetics have unveiled a profound understanding of its mechanisms in tumorigenesis and have offered promising strategies for epigenetic therapy in cancer patients. In our study, through bioinformatics analysis, we discovered a significant downregulation and hypermethylation of FOXI2 in clear cell renal cell carcinoma (ccRCC), while the expression in chromophobe cell carcinoma (chRCC) exhibited the opposite trend. Moreover, we established a strong correlation between FOXI2 expression levels and the prognosis of ccRCC. Gene enrichment analysis and cell function experiments unequivocally demonstrate that FOXI2 possesses the capability to induce cell cycle arrest and inhibit cell proliferation. Our research findings demonstrate that the expression of FOXI2 in ccRCC is under the regulation of promoter hypermethylation. Furthermore, in vitro experiments have conclusively shown that the overexpression of FOXI2 induces cell cycle arrest and inhibits cell proliferation.
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Affiliation(s)
- Shuai Zhou
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Cong Cheng
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Yi xiang Liao
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Li Wang
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Jin min Zeng
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Fang fang Zhou
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Xiu qin Zhang
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
| | - Tao Yang
- Department of Urology, Jing Zhou Hospital Affiliated to Yangtze University, PR China
- The Second Clinical Medical College to Yangtze University, Jing Zhou City 434020, Hubei Province, PR China
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D'Incal C, Van Dijck A, Ibrahim J, De Man K, Bastini L, Konings A, Elinck E, Gozes L, Marusic Z, Anicic M, Vukovic J, Van der Aa N, Mateiu L, Vanden Berghe W, Kooy RF. ADNP dysregulates methylation and mitochondrial gene expression in the cerebellum of a Helsmoortel-Van der Aa syndrome autopsy case. Acta Neuropathol Commun 2024; 12:62. [PMID: 38637827 DOI: 10.1186/s40478-024-01743-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/11/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Helsmoortel-Van der Aa syndrome is a neurodevelopmental disorder in which patients present with autism, intellectual disability, and frequent extra-neurological features such as feeding and gastrointestinal problems, visual impairments, and cardiac abnormalities. All patients exhibit heterozygous de novo nonsense or frameshift stop mutations in the Activity-Dependent Neuroprotective Protein (ADNP) gene, accounting for a prevalence of 0.2% of all autism cases worldwide. ADNP fulfills an essential chromatin remodeling function during brain development. In this study, we investigated the cerebellum of a died 6-year-old male patient with the c.1676dupA/p.His559Glnfs*3 ADNP mutation. RESULTS The clinical presentation of the patient was representative of the Helsmoortel-Van der Aa syndrome. During his lifespan, he underwent two liver transplantations after which the child died because of multiple organ failure. An autopsy was performed, and various tissue samples were taken for further analysis. We performed a molecular characterization of the cerebellum, a brain region involved in motor coordination, known for its highest ADNP expression and compared it to an age-matched control subject. Importantly, epigenome-wide analysis of the ADNP cerebellum identified CpG methylation differences and expression of multiple pathways causing neurodevelopmental delay. Interestingly, transcription factor motif enrichment analysis of differentially methylated genes showed that the ADNP binding motif was the most significantly enriched. RNA sequencing of the autopsy brain further identified downregulation of the WNT signaling pathway and autophagy defects as possible causes of neurodevelopmental delay. Ultimately, label-free quantification mass spectrometry identified differentially expressed proteins involved in mitochondrial stress and sirtuin signaling pathways amongst others. Protein-protein interaction analysis further revealed a network including chromatin remodelers (ADNP, SMARCC2, HDAC2 and YY1), autophagy-related proteins (LAMP1, BECN1 and LC3) as well as a key histone deacetylating enzyme SIRT1, involved in mitochondrial energy metabolism. The protein interaction of ADNP with SIRT1 was further biochemically validated through the microtubule-end binding proteins EB1/EB3 by direct co-immunoprecipitation in mouse cerebellum, suggesting important mito-epigenetic crosstalk between chromatin remodeling and mitochondrial energy metabolism linked to autophagy stress responses. This is further supported by mitochondrial activity assays and stainings in patient-derived fibroblasts which suggest mitochondrial dysfunctions in the ADNP deficient human brain. CONCLUSION This study forms the baseline clinical and molecular characterization of an ADNP autopsy cerebellum, providing novel insights in the disease mechanisms of the Helsmoortel-Van der Aa syndrome. By combining multi-omic and biochemical approaches, we identified a novel SIRT1-EB1/EB3-ADNP protein complex which may contribute to autophagic flux alterations and impaired mitochondrial metabolism in the Helsmoortel-Van der Aa syndrome and holds promise as a new therapeutic target.
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Affiliation(s)
- Claudio D'Incal
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
| | - Anke Van Dijck
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
- Family Medicine and Population Health (FAMPOP), Department of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Joe Ibrahim
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
| | - Kevin De Man
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
| | - Lina Bastini
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
| | - Anthony Konings
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium
| | - Ellen Elinck
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
| | - Lllana Gozes
- The Elton Laboratory for Molecular Neuroendocrinology, Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Adams Super Center for Brain Studies and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Zlatko Marusic
- Clinical Department of Pathology and Cytology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Mirna Anicic
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Jurica Vukovic
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Department of Pediatrics, School of Medicine, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Nathalie Van der Aa
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
| | - Ligia Mateiu
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium
| | - Wim Vanden Berghe
- Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Epigenetic Signaling lab (PPES), Department of Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Antwerp, Belgium.
| | - R Frank Kooy
- Department of Medical Genetics, University of Antwerp, Prins Boudewijnlaan 43/6, 2650, Edegem, Antwerp, Belgium.
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10
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Xiong H, Chen Z, Li Y, Wu Z, Qian D, Chen L, Li Q, Liu H, Chen W, Lin B, Jia Y, Wang C. Pan-cancer analysis of the prognostic and immunological role of FKBP4. Heliyon 2024; 10:e29098. [PMID: 38601662 PMCID: PMC11004885 DOI: 10.1016/j.heliyon.2024.e29098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 03/29/2024] [Accepted: 03/31/2024] [Indexed: 04/12/2024] Open
Abstract
Objectives Our previous studies revealed the significant roles of FK506-binding protein 4 (FKBP4) in tumorigenesis, however, there has been no pan-cancer analysis of FKBP4. Using bioinformatics, the current study reported the expression and prognostic role of FKBP4, and the correlation between FKBP4 and clinicopathological parameters, methylation, molecular network, immunological traits and drug sensitivity. Methods RNA sequencing data, somatic mutation, and related clinical information were obtained from TCGA using UCSC Xena. The association between FKBP4 expression and clinical features was assessed using TISIDB. The relationships between FKBP4 expression and tumour stage, OS, DSS, DFS, and PFS were analysed using univariate cox regression analysis. The radar plots for TMB and MSI were obtained using "Fmsb" R package. UALCAN was used to explore the effect of FKBP4 methylation on tumour and normal samples. CBioportal was used to analyse copy number mutations in FKBP4 Gene expression and drug sensitivity data were downloaded from the CellMiner database. GO analysis was performed for the high and the low expression of FKBP4 compared with the median level of FKBP4 using clusterProfiler4.0. Results FKBP4 expression is significantly upregulated in various types of cancers. Cox regression analysis showed that high FKBP4 levels were correlated with poor OS, DSS, DFS, and PFS in most patients with cancer. Methylation of FKBP4 DNA was upregulated in most cancers, and FKBP4 expression is positively associated with transmethylase expression. FKBP4 and its copy were significantly associated with the expression of immune-infiltrating cells, immune checkpoint genes, immune modulators, TMB, MMR, and MSI. FKBP4 expression levels significantly correlated with 16 different drug sensitivities (all p < 0.05). Conclusions Our pan-cancer bioinformatic analysis revealed a potential mechanism underlying the effects of FKBP4 on the prognosis and progression of various cancers.
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Affiliation(s)
- Hanchu Xiong
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Zihan Chen
- Surgical Intensive Care Unit, First Affiliated Hospital, Zhejiang University, Hangzhou, Zhejiang, 310016, China
| | - Yucheng Li
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Zhuazhua Wu
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Da Qian
- Department of Burn and Plastic Surgery-Hand Surgery, The Changshu Hospital Affiliated to Soochow University, Changshu, Jiangsu, 215000, China
| | - Long Chen
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Qiang Li
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Huaxin Liu
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Weijun Chen
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Baihua Lin
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Yongshi Jia
- Cancer Center, Department of Radiation Oncology, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
| | - Cheng Wang
- Heart Center, Department of Cardiovascular Medicine, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, 310014, China
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11
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Emantoko Dwi Putra S, Martriano Humardani F, Antonius Y, Jonathan J, Thalia Mulyanata L. Epigenetics of Diabetes: A bioinformatic approach. Clin Chim Acta 2024; 557:117856. [PMID: 38490340 DOI: 10.1016/j.cca.2024.117856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/02/2024] [Accepted: 03/04/2024] [Indexed: 03/17/2024]
Abstract
The adaptability of epigenetics offers a compelling research avenue, notably in the context of Type 2 Diabetes Mellitus (T2DM) biomarkers and provides a nuanced approach to managing biological systems for diagnosis. However, challenges such as DNA degradation during methylation studies are prominent, especially with cell-free DNA (cfDNA) which is present in small quantities in plasma, calling for innovative solutions. To tackle these challenges, four methodological approaches have been identified: firstly, selecting an appropriate DNA extraction method and enhancing DNA yield through amplification; secondly, adapting bisulfite modification techniques to minimize DNA degradation; thirdly, utilizing tools capable of working with minimal DNA quantities; and lastly, employing bisulfite-free methylation techniques. A particularly promising approach is the use of Methylated CpG Tandem Amplification and Sequencing (MCTA-Seq) combined with fragmentation analysis. MCTA-Seq, especially when targeting the CGCGCGG motif sequence associated with T2DM, is an underexplored area. In addressing the dearth of the exploration, our in-silico analysis identified 66 genes with the CGCGCGG motif sequence that contribute to the pathophysiology of T2DM. Further analysis revealed five potential target genes for T2DM screening: EP300, SRC, PPARG, CREBBP, and NCOR2. The method can also be integrated into fragment analysis, notable for its ability to differentiate between long and short DNA segments effectively. Such a distinction is a valuable asset in future diagnostic methodologies, particularly relevant in the analysis of cfDNA, where high precision and sensitivity are essential. However, it is crucial to validate these genes with clinical studies to confirm their relevance and effectiveness in T2DM diagnosis.
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Affiliation(s)
| | - Farizky Martriano Humardani
- Bioinformatics Research Center, Malang 65162, Indonesia; Magister in Biomedical Science Program, Faculty of Medicine, Universitas Brawijaya, Malang 65112, Indonesia.
| | - Yulanda Antonius
- Faculty of Biotechnology, University of Surabaya, Surabaya 60292, Indonesia.
| | - Jonathan Jonathan
- Faculty of Biotechnology, University of Surabaya, Surabaya 60292, Indonesia.
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12
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Fang X, Colina Blanco AE, Christl I, Le Bars M, Straub D, Kleindienst S, Planer-Friedrich B, Zhao FJ, Kappler A, Kretzschmar R. Simultaneously decreasing arsenic and cadmium in rice by soil sulfate and limestone amendment under intermittent flooding. Environ Pollut 2024; 347:123786. [PMID: 38484962 DOI: 10.1016/j.envpol.2024.123786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/22/2024] [Accepted: 03/12/2024] [Indexed: 03/19/2024]
Abstract
Water management in paddy soils can effectively reduce the soil-to-rice grain transfer of either As or Cd, but not of both elements simultaneously due to the higher mobility of As under reducing and Cd under oxidizing soil conditions. Limestone amendment, the common form of liming, is well known for decreasing Cd accumulation in rice grown on acidic soils. Sulfate amendment was suggested to effectively decrease As accumulation in rice, especially under intermittent soil flooding. To study the unknown effects of combined sulfate and limestone amendment under intermittent flooding for simultaneously decreasing As and Cd in rice, we performed a pot experiment using an acidic sandy loam paddy soil. We also included a clay loam paddy soil to study the role of soil texture in low-As rice production under intermittent flooding. We found that liming not only decreased rice Cd concentrations but also greatly decreased dimethylarsenate (DMA) accumulation in rice. We hypothesize that this is due to suppressed sulfate reduction, As methylation, and As thiolation by liming in the sulfate-amended soil and a higher share of deprotonated DMA at higher pH which is taken up less readily than protonated DMA. Decreased gene abundance of potential soil sulfate-reducers by liming further supported our hypothesis. Combined sulfate and limestone amendment to the acidic sandy loam soil produced rice with 43% lower inorganic As, 72% lower DMA, and 68% lower Cd compared to the control soil without amendment. A tradeoff between soil aeration and water availability was observed for the clay loam soil, suggesting difficulties to decrease As in rice while avoiding plant water stress under intermittent flooding in fine-textured soils. Our results suggest that combining sulfate amendment, liming, and intermittent flooding can help to secure rice safety when the presence of both As and Cd in coarse-textured soils is of concern.
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Affiliation(s)
- Xu Fang
- Soil Chemistry Group, Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, CHN, ETH Zurich, CH-8092, Zurich, Switzerland.
| | - Andrea E Colina Blanco
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BAYCEER), University of Bayreuth, 95440, Bayreuth, Germany
| | - Iso Christl
- Soil Chemistry Group, Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, CHN, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Maureen Le Bars
- Soil Chemistry Group, Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, CHN, ETH Zurich, CH-8092, Zurich, Switzerland
| | - Daniel Straub
- Quantitative Biology Center (QBiC), University of Tuebingen, 72076, Tuebingen, Germany; Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tuebingen, 72076, Germany
| | - Sara Kleindienst
- Microbial Ecology, Department of Geosciences, University of Tuebingen, 72076, Tuebingen, Germany; Now: Department of Environmental Microbiology, Institute for Sanitary Engineering, Water Quality and Solid Waste Management (ISWA), University of Stuttgart, Stuttgart, 70569, Germany
| | - Britta Planer-Friedrich
- Environmental Geochemistry, Bayreuth Center for Ecology and Environmental Research (BAYCEER), University of Bayreuth, 95440, Bayreuth, Germany
| | - Fang-Jie Zhao
- College of Resources and Environmental Sciences, Nanjing Agricultural University, 210095, Nanjing, China
| | - Andreas Kappler
- Cluster of Excellence: EXC 2124: Controlling Microbes to Fight Infection, Tuebingen, 72076, Germany; Geomicrobiology, Department of Geosciences, Tuebingen University, 72076, Tuebingen, Germany
| | - Ruben Kretzschmar
- Soil Chemistry Group, Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, CHN, ETH Zurich, CH-8092, Zurich, Switzerland
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13
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Ci Y, Zhang Y, Zhang X. Methylated lncRNAs suppress apoptosis of gastric cancer stem cells via the lncRNA-miRNA/protein axis. Cell Mol Biol Lett 2024; 29:51. [PMID: 38600465 PMCID: PMC11005211 DOI: 10.1186/s11658-024-00568-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 03/28/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) play essential roles in the tumorigenesis of gastric cancer. However, the influence of lncRNA methylation on gastric cancer stem cells (GCSCs) remains unclear. METHODS The N6-methyladenosine (m6A) levels of lncRNAs in gastric cancer stem cells were detected by methylated RNA immunoprecipitation sequencing (MeRIP-seq), and the results were validated by MeRIP-quantitative polymerase chain reaction (qPCR). Specific sites of m6A modification on lncRNAs were detected by single-base elongation- and ligation-based qPCR amplification (SELECT). By constructing and transfecting the plasmid expressing methyltransferase-like 3 (METTL3) fused with catalytically inactivated Cas13 (dCas13b) and guide RNA targeting specific methylation sites of lncRNAs, we obtained gastric cancer stem cells with site-specific methylation of lncRNAs. Reverse transcription (RT)-qPCR and Western blot were used for detecting the stemness of treated gastric cancer stem cells. RESULTS The site-specific methylation of PSMA3-AS1 and MIR22HG suppressed apoptosis and promoted stemness of GCSCs. LncRNA methylation enhanced the stability of PSMA3-AS1 and MIR22HG to suppress apoptosis of GCSCs via the PSMA3-AS1-miR-411-3p- or MIR22HG-miR-24-3p-SERTAD1 axis. Simultaneously, the methylated lncRNAs promoted the interaction between PSMA3-AS1 and the EEF1A1 protein or MIR22HG and the LRPPRC protein, stabilizing the proteins and leading to the suppression of apoptosis. The in vivo data revealed that the methylated PSMA3-AS1 and MIR22HG triggered tumorigenesis of GCSCs. CONCLUSIONS Our study revealed the requirement for site-specific methylation of lncRNAs in the tumorigenesis of GCSCs, contributing novel insights into cancer development.
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Affiliation(s)
- Yuan Ci
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao), Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yuan Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao), Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xiaobo Zhang
- College of Life Sciences, Laboratory for Marine Biology and Biotechnology of Pilot National Laboratory for Marine Science and Technology (Qingdao), Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhejiang University, Hangzhou, 310058, People's Republic of China.
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Spadaro A, Sharma A, Dehzangi I. Predicting lysine methylation sites using a convolutional neural network. Methods 2024:S1046-2023(24)00091-4. [PMID: 38604414 DOI: 10.1016/j.ymeth.2024.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/15/2023] [Accepted: 04/07/2024] [Indexed: 04/13/2024] Open
Abstract
Protein lysine methylation is a particular type of post translational modification that plays an important role in both histone and non-histone function regulation in proteins. Deregulation caused by lysine methyltransferases has been identified as the cause of several diseases including cancer as well as both mental and developmental disorders. Identifying lysine methylation sites is a critical step in both early diagnosis and drug design. This study proposes a new Machine Learning method called CNN-Meth for predicting lysine methylation sites using a convolutional neural network (CNN). Our model is trained using evolutionary, structural, and physicochemical-based presentation along with binary encoding. Unlike previous studies, instead of extracting handcrafted features, we use CNN to automatically extract features from different presentations of amino acids to avoid information loss. Automated feature extraction from these representations of amino acids as well as CNN as a classifier have never been used for this problem. Our results demonstrate that CNN-Meth can significantly outperform previous methods for predicting methylation sites. It achieves 96.0%, 85.1%, 96.4%, and 0.65 in terms of Accuracy, Sensitivity, Specificity, and Matthew's Correlation Coefficient (MCC), respectively. CNN-Meth and its source code are publicly available at https://github.com/MLBC-lab/CNN-Meth.
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Affiliation(s)
- Austin Spadaro
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Alok Sharma
- Institute for Integrated and Intelligent Systems, Griffith University, Brisbane, Australia; Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Iman Dehzangi
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States; Department of Computer Science, Rutgers University, Camden, NJ, United States.
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15
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Wang Y, Li Y, Jing Y, Yang Y, Wang H, Ismtula D, Guo C. Tubulin alpha-1b chain was identified as a prognosis and immune biomarker in pan-cancer combing with experimental validation in breast cancer. Sci Rep 2024; 14:8201. [PMID: 38589634 PMCID: PMC11001892 DOI: 10.1038/s41598-024-58982-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024] Open
Abstract
The α-tubulin subtype, Tubulin α-1b chain (TUBA1B), has been shown to influence immune cell infiltration, cancer growth, and survival across various malignancies. However, a comprehensive study has not yet been undertaken examining the immunological and predictive effects of TUBA1B in a pan-carcinoma context. Using data from TCGA, GEO, and other databases, we analyzed TUBA1B expression across various carcinoma types using transcriptional profiling, prognostic implications, genetic and epigenetic alterations, methylation patterns, and immunological significance. To validate our findings, we conducted Western blot analysis to assess TUBA1B protein levels in matched breast cancer tissue samples and performed CCK-8 proliferation assay, flow cytometry, transwell invasion, and migration assays to comprehensively examine the functional impact of TUBA1B on breast cancer cells. Our pan-cancer analysis found TUBA1B upregulation across most tumor types, with varying expression patterns in distinct immune and molecular subtypes. High TUBA1B expression was an independent risk factor and associated with poor prognoses in several cancers, including BRCA, KICH, LGG, LUAD, and MESO. TUBA1B also demonstrates moderate to high diagnostic accuracy in most tumor types. Increased m6A methylation levels were observed in the TUBA1B gene, while its promoter region displayed low methylation levels. TUBA1B's expression impacted some cancers by elevating tumor mutation burden, microsatellite instability, neoantigen formation, immune cell infiltration, and the modulation of immune checkpoints. Functional enrichment analysis highlights TUBA1B's involvement in important cellular processes such as the cell cycle, p53 signaling, cell senescence, programmed cell death, and the regulation of immune-related pathways. Moreover, our study reveals higher TUBA1B protein expression in breast cancer tissues compared to adjacent tissues. In vitro experiments confirm that TUBA1B deletion reduces breast cancer cell proliferation, invasion, and migration while increasing apoptosis. In conclusion, our study suggests that TUBA1B could potentially serve as a diagnostic marker for predicting cancer immunological profiles and survival outcomes and shed light on the expression and role of TUBA1B in breast cancer, providing a solid foundation for considering it as a promising therapeutic target for breast cancer patient treatment.
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Affiliation(s)
- Yiyang Wang
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China
| | - Yongxiang Li
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China
| | - Yubo Jing
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China
| | - Yuqi Yang
- The First Clinical Medical College of Xinjiang Medical University, Urumqi, 830054, China
| | - Haiyan Wang
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China
| | - Dilimulati Ismtula
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China
| | - Chenming Guo
- Department of Breast Surgery, Center of Digestive and Vascular, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, China.
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Tang Q, Yuan Y, Li L, Xu Y, Ji W, Xiao S, Han Y, Miao W, Cai J, You P, Chen M, Ding S, Li Z, Qi Z, Hou W, Luo H. Comprehensive analysis reveals that LTBR is a immune-related biomarker for glioma. Comput Biol Med 2024; 174:108457. [PMID: 38599071 DOI: 10.1016/j.compbiomed.2024.108457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
Glioma is a common malignant brain tumor with great heterogeneity and huge difference in clinical outcomes. Although lymphotoxin (LT) beta receptor (LTBR) has been linked to immune system and response development for decades, the expression and function in glioma have not been investigated. To confirm the expression profile of LTBR, integrated RNA-seq data from glioma and normal brain tissues were analyzed. Functional enrichment analysis, TMEscore analysis, immune infiltration, the correlation of LTBR with immune checkpoints and ferroptosis, and scRNAseq data analysis in gliomas were in turn performed, which pointed out that LTBR was pertinent to immune functions of macrophages in gliomas. In addition, after being trained and validated in the tissue samples of the integrated dataset, an LTBR DNA methylation-based prediction model succeeded to distinguish gliomas from non-gliomas, as well as the grades of glioma. Moreover, by virtue of the candidate LTBR CpG sites, a prognostic risk-score model was finally constructed to guide the chemotherapy, radiotherapy, and immunotherapy for glioma patients. Taken together, LTBR is closely correlated with immune functions in gliomas, and LTBR DNA methylation could serve as a biomarker for diagnosis and prognosis of gliomas.
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Affiliation(s)
- Qisheng Tang
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Yifan Yuan
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Lingjuan Li
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Yue Xu
- Key Laboratory of Shaanxi Province for Craniofacial Precision Medicine Research, Department of General Dentistry, College of Stomatology, Xi'an Jiaotong University, Xi'an, 710004, Shaanxi Province, China
| | - Wei Ji
- Department of Anesthesiology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, 264000, Shandong Province, China
| | - Siyu Xiao
- Department of Rehabilitation, Gongan Hospital of Traditional Chinese Medicine Affiliated to Hubei University of Chinese Medicine, Jingzhou, 434300, Hubei Province, China
| | - Yi Han
- Naval Medical Center of PLA, Naval Medical University, Shanghai, 200052, China
| | - Wenrong Miao
- Naval Medical Center of PLA, Naval Medical University, Shanghai, 200052, China
| | - Jing Cai
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Pu You
- Shanghai QuietD Biotechnology Co., Ltd., Shanghai, 201210, China
| | - Ming Chen
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Saineng Ding
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China
| | - Zhen Li
- Shanghai QuietD Biotechnology Co., Ltd., Shanghai, 201210, China.
| | - Zengxin Qi
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China.
| | - Weiliang Hou
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China.
| | - Hao Luo
- Department of Neurosurgery, Huashan Hospital, Shanghai Medical College, State Key Laboratory of Medical Neurobiology, MOE Frontiers Center for Brain Science and Institutes of Brain Science, Fudan University, Shanghai, 200040, China.
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17
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Budzyńska S, Izdebska A, Bierła K, Budka A, Niedzielski P, Mocek-Płóciniak A, Starzyk J, Mleczek M. Temporal arsenic form changes dynamics and accumulation patterns in Tilia cordata Mill. seedlings: Insights into metalloid transformation and tolerance mechanisms in trees. Chemosphere 2024; 356:141925. [PMID: 38588898 DOI: 10.1016/j.chemosphere.2024.141925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/27/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024]
Abstract
Arsenic (As) remediation is challenging due to the complex nature and the persistence of these metalloid compounds. While it may seem that differences between As forms influence have been extensively described, new findings challenge the previously accepted knowledge, particularly for woody plants. Therefore, this study focused on 2-year-old Tilia cordata Mill. seedlings early (0, 2, 4, 12, 24 h) and late (3, 7, 12, 18, 25, 33 days) responses during growth under: As(III), As(V) or dimethylarsinic acid (DMA) (0.3 mM). Time-dependent transformations of As forms, distribution in plants, and microbiological characteristics (actinobacteria, bacteria, fungi, enzyme activity) were investigated. The highest increase in total As content was observed in plants exposed to As(V) and As(III). Dynamic metalloid form changes in the solution and tree organs were indicated. The most phytotoxic was DMA. This form was the main factor limiting the growth and effective accumulation of As. Despite experimenting in hydroponics, microorganisms played an important role in As form transformations, suggesting the potential for microbial-assisted dendroremediation strategies. The study confirmed that trees can convert more toxic forms into less toxic ones (e.g. As(III) to phytochelatins - As(III)-(PC3)), whose presence in roots seedlings exposed to As(III) and As(V) has been identified. The formation of hydrophobic forms (e.g. dimethylarsinoyl lipid) in the roots of seedlings grown under As(V) was confirmed. It is the first discovery for trees, previously observed only in bacteria and algae. The dynamics of metalloid form changes indicated that T. cordata transforms As forms according to their needs, which may give tree species an advantage in phytoremediation techniques. It holds great promise for the potential of dendroremediation.
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Affiliation(s)
- Sylwia Budzyńska
- Poznań University of Life Sciences, Faculty of Forestry and Wood Technology, Department of Chemistry, Wojska Polskiego 75, 60-625, Poznań, Poland.
| | - Aleksandra Izdebska
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, UMR 5254, IPREM, 64053, Pau, France
| | - Katarzyna Bierła
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, UMR 5254, IPREM, 64053, Pau, France
| | - Anna Budka
- Poznań University of Life Sciences, Faculty of Environmental and Mechanical Engineering, Department of Construction and Geoengineering, Wojska Polskiego 28, 60-637, Poznań, Poland
| | - Przemysław Niedzielski
- Adam Mickiewicz University, Faculty of Chemistry, Uniwersytetu Poznańskiego 8, 61-614, Poznań, Poland
| | - Agnieszka Mocek-Płóciniak
- Poznań University of Life Sciences, Faculty of Agriculture, Horticulture and Bioengineering, Department of Soil Science and Microbiology, Szydłowska 50, 60-637, Poznań, Poland
| | - Justyna Starzyk
- Poznań University of Life Sciences, Faculty of Agriculture, Horticulture and Bioengineering, Department of Soil Science and Microbiology, Szydłowska 50, 60-637, Poznań, Poland
| | - Mirosław Mleczek
- Poznań University of Life Sciences, Faculty of Forestry and Wood Technology, Department of Chemistry, Wojska Polskiego 75, 60-625, Poznań, Poland
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18
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Caplette JN, Wilson SC, Mestrot A. Antimony release and volatilization from organic-rich and iron-rich submerged soils. J Hazard Mater 2024; 470:134230. [PMID: 38608583 DOI: 10.1016/j.jhazmat.2024.134230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
Antimony (Sb) is an poorly understood, increasingly common pollutant, especially in soils susceptible to waterlogging. We investigated the impact of waterlogging on Sb release, methylation, and volatilization from an organic-rich wetland soil and an iron (Fe)-rich floodplain soil in a 27-day microcosm experiment. The release of Sb into the porewaters of the organic-rich soil was environmentally relevant and immediate with waterlogging (3.2 to 3.5 mg L-1), and likely associated with a complex interplay of sulfide precipitation, sorption with organic matter and manganese (Mn) (oxyhydr)oxides in the soil. The release of Sb from the Fe-rich soil was likely associated with Fe-(oxyhydr)oxide reduction and immobilized due to co-precipitation with Fe-sulfides or as Sb-sulfides. Volatile Sb was produced from the soils after waterlogging. The organic-rich soil produced more volatile Sb (409 to 835 ng kgsoil-1), but the Fe-rich soil volatilized Sb more efficiently. The negligible association of Sb volatilization with soil parameters indicates a more complex underlying, potentially microbial, mechanism and that antimony volatilization could be ubiquitous and not dependent on specific soil properties. Future works should investigate the microbial and physiochemical drivers of Sb volatilization in soils as it may be an environmentally relevant part of the biogeochemical cycle.
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Affiliation(s)
- J N Caplette
- Institute of Geography, University of Bern, Switzerland; Minnow Aquatic Environmental Services, Toronto, Canada.
| | - S C Wilson
- School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia
| | - A Mestrot
- Institute of Geography, University of Bern, Switzerland.
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19
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Ahmadpour S, Moshkdanian G, Rezvani Z, Almasi M. L-carnitine fails to rescue chemotherapy injured ovaries by epigenetic changes of transcription factors. Gene 2024; 901:148128. [PMID: 38181927 DOI: 10.1016/j.gene.2024.148128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 11/14/2023] [Accepted: 01/02/2024] [Indexed: 01/07/2024]
Abstract
Cyclophosphamide (CP), as an anti-cancer drug, is frequently used to treat various types of cancer. A decreased number of ovarian follicles impaired normal ovarian function, and subsequent premature ovarian failure (POF) presented as a side effect of cyclophosphamide usage. These events may eventually affect the fertility rate of individuals. The present study showed the effect of cyclophosphamide on ovarian reserves and the protective effect of L-carnitine (LC) as an antioxidant to prevent POF. To design the study, six to eight-week-old NMRI female mice were divided into three groups: control, cyclophosphamide (CP), and cyclophosphamide + L-carnitine (CP + LC). Mice received drugs intraperitoneally (IP) for 21 days. In the following 24 h after the last injection, both ovaries were used to evaluate the expression of Sohlh1 and Lhx8 genes by Real-time PCR. Furthermore, the alteration of Lhx8 promoter methylation was examined by Methylation-sensitive high-resolution melting analysis (MS-HRM). The present data showed the negative effect of CP on regulator genes of oogenesis including Sohlh1 and Lhx8. In addition, an examination of the epigenetic status of the Lhx8 gene showed a change in promoter methylation of this gene following cyclophosphamide injection. Although, L-carnitine is an effective antioxidant in relieving oxidative stress caused by cyclophosphamide and its damage, in the present study, however, the use of L-carnitine failed to protect the ovaries from changes caused by CP injection. So, using cyclophosphamide can alter the expression of folliculogenesis genes through its effects on epigenetic changes and may cause POF. The results of the present study showed that L-carnitine consumption can't protect the ovaries against the adverse effects of CP.
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Affiliation(s)
- Sara Ahmadpour
- Biotechnology Department, Faculty of Chemistry, University of Kashan, Kashan, Iran
| | - Ghazaleh Moshkdanian
- Gametogenesis Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Science, Kashan, Iran.
| | - Zahra Rezvani
- Department of Cell and Molecular Biology, Faculty of Chemistry, University of Kashan, Iran
| | - Majid Almasi
- Gametogenesis Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Science, Kashan, Iran
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20
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Hench J, Hultschig C, Brugger J, Mariani L, Guzman R, Soleman J, Leu S, Benton M, Stec IM, Hench IB, Hoffmann P, Harter P, Weber KJ, Albers A, Thomas C, Hasselblatt M, Schüller U, Restelli L, Capper D, Hewer E, Diebold J, Kolenc D, Schneider UC, Rushing E, Della Monica R, Chiariotti L, Sill M, Schrimpf D, von Deimling A, Sahm F, Kölsche C, Tolnay M, Frank S. EpiDiP/NanoDiP: a versatile unsupervised machine learning edge computing platform for epigenomic tumour diagnostics. Acta Neuropathol Commun 2024; 12:51. [PMID: 38576030 PMCID: PMC10993614 DOI: 10.1186/s40478-024-01759-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/11/2024] [Indexed: 04/06/2024] Open
Abstract
DNA methylation analysis based on supervised machine learning algorithms with static reference data, allowing diagnostic tumour typing with unprecedented precision, has quickly become a new standard of care. Whereas genome-wide diagnostic methylation profiling is mostly performed on microarrays, an increasing number of institutions additionally employ nanopore sequencing as a faster alternative. In addition, methylation-specific parallel sequencing can generate methylation and genomic copy number data. Given these diverse approaches to methylation profiling, to date, there is no single tool that allows (1) classification and interpretation of microarray, nanopore and parallel sequencing data, (2) direct control of nanopore sequencers, and (3) the integration of microarray-based methylation reference data. Furthermore, no software capable of entirely running in routine diagnostic laboratory environments lacking high-performance computing and network infrastructure exists. To overcome these shortcomings, we present EpiDiP/NanoDiP as an open-source DNA methylation and copy number profiling suite, which has been benchmarked against an established supervised machine learning approach using in-house routine diagnostics data obtained between 2019 and 2021. Running locally on portable, cost- and energy-saving system-on-chip as well as gpGPU-augmented edge computing devices, NanoDiP works in offline mode, ensuring data privacy. It does not require the rigid training data annotation of supervised approaches. Furthermore, NanoDiP is the core of our public, free-of-charge EpiDiP web service which enables comparative methylation data analysis against an extensive reference data collection. We envision this versatile platform as a useful resource not only for neuropathologists and surgical pathologists but also for the tumour epigenetics research community. In daily diagnostic routine, analysis of native, unfixed biopsies by NanoDiP delivers molecular tumour classification in an intraoperative time frame.
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Affiliation(s)
- Jürgen Hench
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland.
| | - Claus Hultschig
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Jon Brugger
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Luigi Mariani
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Raphael Guzman
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Jehuda Soleman
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Severina Leu
- Klinik für Neurochirurgie, Universitätsspital Basel, Spitalstrasse 21, 4031, Basel, Switzerland
| | - Miles Benton
- Human Genomics, Institute of Environmental Science and Research (ESR), 5022, Porirua, Wellington, New Zealand
| | - Irenäus Maria Stec
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Ivana Bratic Hench
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Per Hoffmann
- Life&Brain GmbH, Venusberg-Campus 1, Gebäude 76, 53127, Bonn, Germany
| | - Patrick Harter
- Institute of Neuropathology, Center for Neuropathology and Prion Research, Feodor- Lynen-Str. 23, 81377, München, Germany
| | - Katharina J Weber
- Neurological Institute (Edinger Institute), University Hospital, Heinrich-Hoffmann- Straße 7, 60528, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Anne Albers
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Pottkamp 2, 48149, Münster, Germany
| | - Ulrich Schüller
- Forschungsinstitut Kinderkrebszentrum, Martinistrasse 52, 20251, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, University Hospital Hamburg- Eppendorf, Hamburg, Germany
- Institute of Neuropathology, University Hospital Hamburg-Eppendorf, Hamburg, Germany
- Department of Neuropathology, Department of Neuropathology, Charité- Universitätsmedizin Berlin, Charitéplatz 1, 10117, Berlin, Germany
| | - Lisa Restelli
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - David Capper
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Ekkehard Hewer
- Institut universitaire de pathologie, Lausanne University Hospital (CHUV), University of Lausanne, Rue du Bugnon 25, 1011, Lausanne, Switzerland
| | - Joachim Diebold
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Danijela Kolenc
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
| | - Ulf C Schneider
- Klinik für Neurochirurgie, Luzerner Kantonsspital, Haus 31, 6000, 16, Spitalstrasse, Luzern, Switzerland
| | - Elisabeth Rushing
- , 15. Luzerner Kantonsspital, Pathologie, Haus 27, 6000, Spitalstrasse, Luzern 16, Switzerland
- Medica Pathologie Zentrum Zürich, Hottingerstrasse 9 / 11, 8032, Zürich, Switzerland
| | - Rosa Della Monica
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486 - 80145, Napoli, Italy
| | - Lorenzo Chiariotti
- CEINGE-Biotecnologie Avanzate, Via Gaetano Salvatore, 486 - 80145, Napoli, Italy
| | - Martin Sill
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neurooncology, German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Felix Sahm
- Department of Neuropathology, Institute of Neuropathology, University Hospital Heidelberg, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- CCU Neuropathology, German Consortium for Translational Cancer Research (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- , 23. DKFZ, Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Christian Kölsche
- Pathologisches Institut der LMU, Thalkirchner Str. 36, 80337, München, Germany
| | - Markus Tolnay
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland
| | - Stephan Frank
- Institut für Medizinische Genetik und Pathologie, Universitätsspital Basel, Schönbeinstr. 40, 4031, Basel, Switzerland.
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21
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Zhang C, Xu X, Wang T, Lu Y, Lu Z, Wang T, Pan Z. Clinical performance and utility of a noninvasive urine-based methylation biomarker: TWIST1/Vimentin to detect urothelial carcinoma of the bladder. Sci Rep 2024; 14:7941. [PMID: 38575639 PMCID: PMC10995167 DOI: 10.1038/s41598-024-58586-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 04/01/2024] [Indexed: 04/06/2024] Open
Abstract
Traditional clinical modalities for diagnosing bladder urothelial carcinoma (BUC) remain limited due to their invasive nature, significant costs, discomfort associated with cystoscopy, and low sensitivity to urine cytology. Therefore, there is an urgent need to identify highly sensitive, specific, and noninvasive biomarkers for the early detection of this neoplasm. Hypermethylated TWIST1/Vimentin promoter may be a noninvasive biomarker using urine sample. We assessed the TWIST1/Vimentin promoter methylation status in urine samples using the Methylated Human TWIST1 and Vimentin Gene Detection Kit (Jiangsu MicroDiag Biomedicine Co., Ltd., China). The samples were collected from five groups: group 1 consisted of patients with BUC, group 2 contained other patients with urologic tumors, group 3 consisted of patients with benign diseases (e.g., urinary tract infections, lithiasis, and benign prostatic hyperplasia), Group 4 included UTUC (upper tract urothelial carcinoma) patients and group5 comprised healthy individuals. The study encompassed 77 BUC patients, and we evaluated the degree of methylation of the TWIST1/Vimentin gene in their urine samples. Notably, TWIST1/Vimentin positivity was significantly elevated in comparison to groups 2, 3 and 5 (all p < 0.001) at a rate of 77.9%, but no significant difference was observed when compared to group 4. In the relationship between TWIST1/Vimentin methylation and clinicopathological features of BC patients from our center, we found there was no significant association between TWIST1/Vimentin status and proteinuria and/or hematuria, and hypermethylation of TWIST1 / VIM genes was found in both high and low tumor grade and in both non-muscle invasive bladder cancer (stages Tis, Ta, or T1) and muscle-invasive bladder cancer (stage T2 or above). In the multivariable analysis for cancer detection, a positive TWIST1/Vimentin methylation were significantly linked to a heightened risk of BC. Moreover, TWIST1/Vimentin promoter methylation demonstrated an ability to detect BUC in urine samples with a sensitivity of 78% and a specificity of 83%. Our findings reveal that hypermethylation of the TWIST1/Vimentin promoter occurs in bladder urothelial carcinoma, and its high sensitivity and specificity suggest its potential as a screening and therapeutic biomarker for urothelial carcinoma of the bladder.
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Affiliation(s)
- Chanchan Zhang
- Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang , China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Xiaohong Xu
- Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang , China
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China
| | - Tao Wang
- Jiangsu MicroDiag Biomedicine Co., Ltd., Suzhou, China
| | - Yan Lu
- Jiangsu MicroDiag Biomedicine Co., Ltd., Suzhou, China
| | - Zhiheng Lu
- Jiangsu MicroDiag Biomedicine Co., Ltd., Suzhou, China
| | - Tuantuan Wang
- Jiangsu MicroDiag Biomedicine Co., Ltd., Suzhou, China
| | - Zhiwen Pan
- Zhejiang Cancer Hospital, Hangzhou, 310022, Zhejiang , China.
- Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, Zhejiang, China.
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22
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Kinoshita R, Inoue N, Iwatani Y, Noguchi Y, Hidaka Y, Watanabe M. Methylation levels of the IL10 gene in peripheral blood are related to the intractability of Graves' disease. Clin Immunol 2024; 263:110196. [PMID: 38570004 DOI: 10.1016/j.clim.2024.110196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 02/28/2024] [Accepted: 03/18/2024] [Indexed: 04/05/2024]
Abstract
The prognosis of autoimmune thyroid diseases (AITDs), including Hashimoto's disease (HD) and Graves' disease (GD), is difficult to predict. DNA methylation regulates gene expression of immune mediating factors. Interleukin (IL)-10 is a Th2 cytokine that downregulates inflammatory cytokines produced by Th1 cells. To clarify the role of methylation of the IL10 gene in the prognosis of AITD, we evaluated the methylation levels of two CpG sites in the IL10 promoter using pyrosequencing. The methylation levels of the -185 CpG site of the IL10 gene were related to age and GD intractability in GD patients. Furthermore, the C carrier of the IL10-592 A/C polymorphism was related to low methylation levels of the -185 CpG site. The methylation levels of the IL10-185 CpG site of the IL10 gene were related to the intractability of GD and were lower in individuals with the C allele of the IL10-592 A/C polymorphism.
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Affiliation(s)
- Riku Kinoshita
- Department of Clinical Laboratory and Biomedical Sciences, Division of Health Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7 Suita, Osaka 565-0871, Japan
| | - Naoya Inoue
- Department of Clinical Laboratory and Biomedical Sciences, Division of Health Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7 Suita, Osaka 565-0871, Japan; Laboratory for Clinical Investigation, Osaka University Hospital, Yamadaoka 2-15, Suita, Osaka 565-0871, Japan
| | - Yoshinori Iwatani
- Department of Clinical Laboratory and Biomedical Sciences, Division of Health Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7 Suita, Osaka 565-0871, Japan
| | - Yusuke Noguchi
- Department of Clinical Laboratory and Biomedical Sciences, Division of Health Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7 Suita, Osaka 565-0871, Japan
| | - Yoh Hidaka
- Laboratory for Clinical Investigation, Osaka University Hospital, Yamadaoka 2-15, Suita, Osaka 565-0871, Japan
| | - Mikio Watanabe
- Department of Clinical Laboratory and Biomedical Sciences, Division of Health Sciences, Osaka University Graduate School of Medicine, Yamadaoka 1-7 Suita, Osaka 565-0871, Japan.
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23
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Gonzalez T, Nie Q, Chaudhary LN, Basel D, Reddi HV. Methylation signatures as biomarkers for non-invasive early detection of breast cancer: A systematic review of the literature. Cancer Genet 2024; 282-283:1-8. [PMID: 38134587 DOI: 10.1016/j.cancergen.2023.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023]
Abstract
BACKGROUND Early detection of breast cancer would help alleviate the burden of treatment for early-stage breast cancer and help patient prognosis. There is currently no established gene panel that utilizes the potential of DNA methylation as a molecular signature for the early detection of breast cancer. This systematic review aims to identify the optimal methylation biomarkers for a non-invasive liquid biopsy assay and the gaps in knowledge regarding biomarkers for early detection of breast cancer. METHODS Following the PRISMA-ScR method, Pubmed and Google Scholar was searched for publications related to methylation biomarkers in breast cancer over a five-year period. Eligible publications were mined for key data fields such as study aims, cohort demographics, types of breast cancer studied, technologies used, and outcomes. Data was analyzed to address the objectives of the review. RESULTS Literature search identified 112 studies of which based on eligibility criteria, 13 studies were included. 28 potential methylation gene targets were identified, of which 23 were methylated at the promoter region, 1 was methylated in the body of the gene and 4 were methylated at yet to be identified locations. CONCLUSIONS Our evaluation shows that at minimum APC, RASSFI, and FOXA1 genes would be a promising set of genes to start with for the early detection of breast cancer, based on the sensitivity and specificity outlined in the studies. Prospective studies are needed to optimize biomarkers for broader impact in early detection of breast cancer.
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Affiliation(s)
- Tessa Gonzalez
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA
| | - Qian Nie
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA
| | - Lubna N Chaudhary
- Division of Division of Hematology/Oncology, Department of Medicine, Medical College of Wisconsin, CT, USA
| | - Donald Basel
- Division of Genetics, Department of Pediatrics, Medical College of Wisconsin, CT, USA
| | - Honey V Reddi
- Division of Precision Medicine and Cytogenetics, Department of Pathology, Medical College of Wisconsin, CT, USA.
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24
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Aanniz T, Bouyahya A, Balahbib A, El Kadri K, Khalid A, Makeen HA, Alhazmi HA, El Omari N, Zaid Y, Wong RSY, Yeo CI, Goh BH, Bakrim S. Natural bioactive compounds targeting DNA methyltransferase enzymes in cancer: Mechanisms insights and efficiencies. Chem Biol Interact 2024; 392:110907. [PMID: 38395253 DOI: 10.1016/j.cbi.2024.110907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/06/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024]
Abstract
The regulation of gene expression is fundamental to health and life and is essentially carried out at the promoter region of the DNA of each gene. Depending on the molecular context, this region may be accessible or non-accessible (possibility of integration of RNA polymerase or not at this region). Among enzymes that control this process, DNA methyltransferase enzymes (DNMTs), are responsible for DNA demethylation at the CpG islands, particularly at the promoter regions, to regulate transcription. The aberrant activity of these enzymes, i.e. their abnormal expression or activity, can result in the repression or overactivation of gene expression. Consequently, this can generate cellular dysregulation leading to instability and tumor development. Several reports highlighted the involvement of DNMTs in human cancers. The inhibition or activation of DNMTs is a promising therapeutic approach in many human cancers. In the present work, we provide a comprehensive and critical summary of natural bioactive molecules as primary inhibitors of DNMTs in human cancers. The active compounds hold the potential to be developed as anti-cancer epidrugs targeting DNMTs.
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Affiliation(s)
- Tarik Aanniz
- Medical Biotechnology Laboratory, Rabat Medical & Pharmacy School, Mohammed V University in Rabat, Rabat, B.P, 6203, Morocco.
| | - Abdelhakim Bouyahya
- Laboratory of Human Pathologies Biology, Faculty of Sciences, Mohammed V University in Rabat, Rabat, 10106, Morocco.
| | - Abdelaali Balahbib
- High Institute of Nursing Professions and Health Techniques of Errachidia, Errachidia, Morocco.
| | - Kawtar El Kadri
- High Institute of Nursing Professions and Health Techniques of Errachidia, Errachidia, Morocco
| | - Asaad Khalid
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan, Saudi Arabia; Medicinal and Aromatic Plants Research Institute, National Center for Research, P.O. Box: 2424, Khartoum, 11111, Sudan.
| | - Hafiz A Makeen
- Pharmacy Practice Research Unit, Clinical Pharmacy Department, Faculty of Pharmacy, Jazan University, Jazan, Saudi Arabia.
| | - Hassan A Alhazmi
- Substance Abuse and Toxicology Research Center, Jazan University, P.O. Box: 114, Jazan, Saudi Arabia; Pharmacy Practice Research Unit, Clinical Pharmacy Department, Faculty of Pharmacy, Jazan University, Jazan, Saudi Arabia.
| | - Nasreddine El Omari
- High Institute of Nursing Professions and Health Techniques of Tetouan, Tetouan, Morocco.
| | - Younes Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University in Rabat, Morocco.
| | - Rebecca Shin-Yee Wong
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia; Department of Medical Education, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia.
| | - Chien Ing Yeo
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia.
| | - Bey Hing Goh
- Sunway Biofunctional Molecules Discovery Centre, School of Medical and Life Sciences, Sunway University Malaysia, Bandar Sunway, 47500, Selangor Darul Ehsan, Malaysia; Biofunctional Molecule Exploratory Research Group, School of Pharmacy, Monash University Malaysia, Bandar Sunway, 47500, Malaysia; College of Pharmaceutical Sciences, Zhejiang University, 310058, Hangzhou, Zhejiang, China.
| | - Saad Bakrim
- Geo-Bio-Environment Engineering and Innovation Laboratory, Molecular Engineering, Biotechnology and Innovation Team, Polydisciplinary Faculty of Taroudant, Ibn Zohr University, Agadir, 80000, Morocco.
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Mao Y, Miao J, Xi L, Tong H, Shen X, Li Q, Yu C. circSKA3 promotes colorectal cancer metastases through miR-1238 and methylation. Mol Cell Biochem 2024; 479:941-950. [PMID: 37256443 PMCID: PMC11015993 DOI: 10.1007/s11010-023-04773-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 05/18/2023] [Indexed: 06/01/2023]
Abstract
Colorectal cancer (CRC) is becoming one of the most common cancers overworld, which causes a high rate of death in patients. circRNAs are non-coding RNAs(ncRNAs), which have been reported to be involved in the development of many cancers, including CRC. However, the exact mechanism that how circRNAs function through in CRC remains unclear. In this study, we firstly used GEO database and bioinformatic methods to identify the significant changed circRNAs, with circSKA3 being the most significantly upregulated circRNAs in CRC tissues. PCR results further confirmed higher expression of circSKA3 in CRC patients. CCK-8, scratch, and transwell assays indicated that circSKA3 could promote the proliferation, migration, and invasion of CRC cell lines for cell detection. Dual-luciferase assays were carried out to detect the downstream targets of circSKA3, and a binding site between circSKA3 and miR-1238 was identified and miR-1238 could also combine with YTHDF2. Overexpression of YTHDF2 rescued the decreased cell proliferation, migration, and invasion caused by miR-1238 overexpression. RIP assay further indicated that YTHDF2 could decrease the methylation of STAT5A. In summary, our study found that circSKA3 was upregulated in CRC tissues comparing with normal tissues. circSKA3 could increase the expression ofYTHDF2 through sponging miR-1238 to decrease the methylation of STAT5A, which could provide a novel target for CRC treatment.
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Affiliation(s)
- Yonghuan Mao
- Department of General Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210008, China
- Department of General Surgery, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, China
| | - Ji Miao
- Department of General Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210008, China
| | - Ling Xi
- Department of Gerontology, Jiangsu Province Official Hospital, Nanjing, 210009, China
| | - Hanwen Tong
- Department of Emergency, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210008, China
| | - Xiaofei Shen
- Department of General Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210008, China.
| | - Qiang Li
- Department of General Surgery, Nanjing Drum Tower Hospital Clinical College of Nanjing Medical University, Nanjing, 210008, China.
| | - Chunzhao Yu
- Department of General Surgery, the Second Affiliated Hospital of Nanjing Medical University, Nanjing, 210011, China.
- Department of General Surgery, Sir Run Run Hospital of Nanjing Medical University, Nanjing, 211112, China.
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Gosnell KJ, Mazrui N, Mason RP. Properties influencing flux and diatom uptake of mercury and methylmercury from estuarine sediments. Environ Pollut 2024; 346:123604. [PMID: 38423275 DOI: 10.1016/j.envpol.2024.123604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Mercury (Hg) is a conspicuous and persistent global pollutant. Ionic Hg can be methylated into noxious methylmercury (CH3Hg), which biomagnifies in marine tropic webs and poses a health risk to humans and organisms. Sediment Hg methylation rates are variable, and the output flux of created CH3Hg are dependent on sediment characteristics and environmental factors. Thus, uncertainties remain about the formation and flux of CH3Hg from sediment, and how this could contribute to the bioaccumulative burden for coastal organisms in shallow ecosystems. Cores were collected from 3 estuarine locations along the Eastern USA to examine how sediments characteristics influence the introduction of Hg and CH3Hg into the base of the food chain. Stable isotopes of inorganic 200Hg and CH3199Hg were injected into sediments of individual cores, with cultured diatoms constrained to overlying waters. Five different treatments were done on duplicate cores, spiked with: (1) no Hg isotopes (control); (2) inorganic 200Hg; (3) CH3199Hg; (4) both 200Hg and CH3199Hg isotopes, (5) both 200Hg and CH3199Hg into overlying waters (not sediment). Experimental cores were incubated for 3 days under temperature and light controlled conditions. These results demonstrate that upper sediments characteristics lead to high variability in Hg cycling. Notably, sediments which contained abundant and peaty organic material (∼28 %LOI), had the highest pore water DOC (3206 μM) and displayed bands of sulfur reducing bacteria yielded the greatest methylation rate (1.97 % day-1) and subsequent diatom uptake of CH3200Hg (cell quota 0.18 amol/cell) in the overlying water.
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Affiliation(s)
- Kathleen J Gosnell
- GEOMAR Helmholtz Centre for Ocean Research Kiel, Kiel, Germany; Department of Marine Sciences, University of Connecticut, Groton, CT, USA.
| | - Nashaat Mazrui
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA; Okavango Research Institute, University of Botswana, Manu, Botswana
| | - Robert P Mason
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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Barrio E, Lerma-Puertas D, Jaulín-Pueyo JJ, Labarta JI, Gascón-Catalán A. Epigenetic modifications in the ferroptosis pathway in cord blood cells from newborns of smoking mothers and their influence on fetal growth. Reprod Toxicol 2024; 125:108581. [PMID: 38552991 DOI: 10.1016/j.reprotox.2024.108581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/12/2024] [Accepted: 03/22/2024] [Indexed: 04/01/2024]
Abstract
Maternal smoking during pregnancy increases oxidative stress and decreases antioxidant capacity in newborns. Uncontrolled oxidative stress plays a role in fetal development disorders and in adverse perinatal outcomes. In order to identify molecular pathways involved in low fetal growth, epigenetic modifications in newborns of smoking and non-smoking mothers were examined. Low birth weight newborns of mothers who smoked more than 10 cigarettes per day during the first trimester of pregnancy and normal birth weight newborns of mothers who did not smoke during pregnancy were included in the study. DNA was extracted from umbilical cord blood of term newborns. 125 differentially methylated regions were identified by MeDIP-Seq. Functional analysis revealed several pathways, such as ferroptosis, that were enriched in differentially methylated genes after prenatal smoke exposure. GPX4 and PCBP1 were found to be hypermethylated and associated with low fetal growth. These epigenetic modifications in ferroptosis pathway genes in newborns of smoking mothers can potentially contribute to intrauterine growth restriction through the induction of cell death via lipid peroxidation of cell membranes. The identification of epigenetic modifications in the ferroptosis pathway sheds light on the potential mechanisms underlying the pathophysiology of low birth weight in infants born to smoking mothers.
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Affiliation(s)
- Eva Barrio
- Facultad de Medicina, Universidad de Zaragoza, Spain
| | - Diego Lerma-Puertas
- Facultad de Medicina, Universidad de Zaragoza, Spain; Servicio de Obstetricia y Ginecología, Hospital Universitario Clínico Lozano Blesa, Zaragoza, Spain
| | - José Javier Jaulín-Pueyo
- Facultad de Medicina, Universidad de Zaragoza, Spain; Servicio de Pediatría. Hospital Universitario Miguel Servet, Zaragoza, Spain
| | - José Ignacio Labarta
- Facultad de Medicina, Universidad de Zaragoza, Spain; Servicio de Pediatría. Hospital Universitario Miguel Servet, Zaragoza, Spain
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Izaguirre N, Erdocia X, Labidi J. Exploring chemical reactions to enhance thermal and dispersion stability of kraft and organosolv lignin. Int J Biol Macromol 2024; 264:130518. [PMID: 38428757 DOI: 10.1016/j.ijbiomac.2024.130518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/03/2024]
Abstract
Lignin has been overlooked and used as a waste for long due to its complex and partially hydrophobic structure. Many efforts have been carried out to overcome these deficiencies and apply it as a high-value product, which are insufficient to reach the full potential of lignin in various advanced applications, since they require with procedures for the obtaining of more specific and fine-tuned chemical structures. This work focuses on the obtaining of differently structured hydrophilic lignins derived both from Kraft and organosolv isolation processes. The chemical structures of the different lignin types were studied, and the effect of the structural differences in the modification processes and their subsequent properties analyzed, valorizing their potential application for diverse purposes. The carboxymethylation and sulfomethylation reactions were carried out with the aim of enhancing the polarity of the lignin samples, while the methylation reaction aimed to obtain lignins with higher stability. The physicochemical analyses of the samples, carried out by FTIR, GPC, 31P NMR, 13C NMR, and HSQC NMR, verified the effectiveness of the chemical reactions and conditions selected, obtaining lignins with lower hydroxyl content, due to their substitution and insertion of carboxymetyl, sulfomethyl and methyl groups, therefore obtaining more condensed, aromatic and oxygenated aromatic carbon structures. While the methylation reaction was the most efficient in substituting the OH groups, due to its non-selectivity, OL showed higher modification yields than KL. In terms of the thermal and morphological properties, analyzed by DLS and TGA respectively, it was observed that the modified samples showed lower Z potential values, along with higher conductivity, being the sulfomethylated organosolv lignin the one showing the best results, which was also the one with the smallest particle size and polydispersity index. Finally, all the modified samples showed higher T50% values, suggesting a better stability towards degradation.
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Affiliation(s)
- Nagore Izaguirre
- Biorefinery Processes Research Group, Chemical and Environmental Engineering Department, Engineering Faculty of Gipuzkoa, University of the Basque Country UPV/EHU, Plaza Europa 1, 20018 Donostia, Spain
| | - Xabier Erdocia
- Biorefinery Processes Research Group, Department of Applied Mathematics, University of the Basque Country UPV/EHU, Rafael Moreno "Pichichi" 3, 48013 Bilbao, Spain
| | - Jalel Labidi
- Biorefinery Processes Research Group, Chemical and Environmental Engineering Department, Engineering Faculty of Gipuzkoa, University of the Basque Country UPV/EHU, Plaza Europa 1, 20018 Donostia, Spain.
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Xuekelati S, Maimaitiwusiman Z, Bai X, Xiang H, Li Y, Wang H. Sarcopenia is associated with hypo methylation of TWEAK and increased plasma levels of TWEAK and its downstream inflammatory factor TNF-α in older adults: A case-control study. Exp Gerontol 2024; 188:112390. [PMID: 38437928 DOI: 10.1016/j.exger.2024.112390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/25/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
BACKGROUND Sarcopenia is a harmful condition common among older adults for which no treatment is available. Tumor necrosis factor (TNF)-like weak inducer of apoptosis (TWEAK) and its receptor fibroblast growth factor inducible 14 (FN14) are known to play important roles in the pathogenesis of sarcopenia. This study investigated alterations in methylation in TWEAK and Fn14 to identify potential targets for the managing sarcopenia. MATERIALS AND METHODS Through an epidemiological investigation, we detected methylation of CpG islands (CpGs) in TWEAK and Fn14 in community-dwelling older adult of Xinjiang by bisulfite sequencing. Significant CpGs associated with sarcopenia were selected for detection in 152 older individuals by pyrosequencing. Associations between CpG methylation, plasma inflammatory marker levels, and sarcopenia were analyzed. RESULTS Of 38 CpGs in TWEAK and 30 CpGs in Fn14 detected in 60 individuals, 6 CpGs showed lower methylation in sarcopenia patients compared with control individuals. In 152 older adults, covariance analysis with adjustment for age, gender, triglyceride level, obesity, diabetes, and hypertension showed that the methylation levels of 6 CpGs (CpG8, CpG12, CpG13, CpG20 and CpG21of TWEAK, and CpG24 of Fn14) were significantly lower in sarcopenia patients than in control individuals. With adjustment for additional confounding factors, covariate variance analysis showed that plasma TWEAK, TNF-α and IL-10 levels in the sarcopenia group were significant higher than those in the control group (P = 0.007, P < 0.001, P = 0.003). Multivariate logistic regression analysis showed that CpG8, CpG13, CpG21, and total methylation of TWEAK (OR = 0.767, 95 % CI = 0.622-0.947; OR = 0.740, 95 % CI = 0.583-0.941; OR = 0.734, 95 % CI = 0.561-0.958; OR = 0.883, 95 % CI = 0.795-0.980) as well as CpG22 and total methylation of Fn14 were significantly associated with sarcopenia (OR = 826, 95 % CI = 0.704-0.968; OR = 0.918, 95 % CI = 0.852-0.989). From partial correlation analysis, plasma TWEAK was correlated with plasma TNF-α (r = 0.172, P = 0.042). CONCLUSION Sarcopenia is associated with hypomethylation of TWEAK and increased plasma levels of TWEAK and its downstream inflammatory factor TNF-α in a community-dwelling population of older adults in Xinjiang.
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Affiliation(s)
- Saiyare Xuekelati
- Second Department of Comprehensive Internal Medicine of People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, China
| | - Zhuoya Maimaitiwusiman
- Second Department of Comprehensive Internal Medicine of People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, China
| | - Xue Bai
- Second Department of Comprehensive Internal Medicine of People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, China
| | - Hong Xiang
- Second Department of Comprehensive Internal Medicine of People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, China
| | - Yangjing Li
- Second Department of Comprehensive Internal Medicine of People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, China
| | - Hongmei Wang
- Second Department of Comprehensive Internal Medicine of People's Hospital of Xinjiang Uygur Autonomous Region, Urumqi 830001, China.
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Wang T, Huang J, Chen G, Fu J, Li T, Zou X, Yi H. miR-1293 suppresses osteosarcoma progression by modulating drug sensitivity in response to cisplatin treatment. Int Immunopharmacol 2024; 130:111702. [PMID: 38367464 DOI: 10.1016/j.intimp.2024.111702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/13/2024] [Accepted: 02/13/2024] [Indexed: 02/19/2024]
Abstract
Chemotherapy is considered the primary treatment for osteosarcoma. however, its effectiveness is limited due to drug resistance and toxicity. Thus, identifying novel therapeutic targets to enhance the efficacy of chemotherapy is urgently needed. Here, we identified a novel cisplatin-sensitivity enhancing mechanism via up-regulation of the tumour suppressor gene, miR-1293. Meanwhile, higher levels of miR-1293 observed in prechemotherapy patients were associated with a more favorable prognosis. The mechanism underlying cisplatin upregulated miR-1293 expression involves hypomethylation of the miR-1293 promoter, which blocks the binding of the transcription repressor TFAP2A to the promoter. Furthermore, miR-1293 inhibits osteosarcoma progression by targeting TIMP1 to inactivate the Notch1/Hes1 and TGFBR1/Smad2/3 pathways, thereby promoting tumour cell death. The findings presented herein unveil a novel mechanism for enhancing cisplatin sensitivity and proposed a potential therapeutic strategy for osteosarcoma through pre-chemotherapy supplementation of miR-1293.
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Affiliation(s)
- Tingxuan Wang
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Department of Spinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510005, China
| | - Jincheng Huang
- Department of Orthopedics, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou 450000, China.
| | - Gang Chen
- Department of Orthopedics, Xiangyang Central Hospital, Affiliated Hospital of Hubei University of Arts and Science, Xiangyang 441000, China
| | - Jiahui Fu
- Department of Fetal Medicine and Prenatal Diagnosis, Zhujiang Hospital, Southern Medical University, Guangzhou 510005, China
| | - Tian Li
- School of Basic Medicine, Fourth Military Medical University, Xi'an 10032, China.
| | - Xuenong Zou
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Department of Spinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510005, China.
| | - Hualin Yi
- Guangdong Provincial Key Laboratory of Orthopedics and Traumatology, Department of Spinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510005, China; Guangzhou National Laboratory, Guangzhou 510005, China.
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Li D, Yang W, Pang J, Yu G. Differential DNA methylation landscape of miRNAs genes in mice liver fibrosis. Mol Biol Rep 2024; 51:475. [PMID: 38553662 DOI: 10.1007/s11033-024-09416-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/05/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Patients with chronic liver disease were found nearly all to have liver fibrosis, which is characterized by excess accumulation of extracellular matrix (ECM) proteins. While ECM accumulation can prevent liver infection and injury, it can destroy normal liver function and architecture. miRNA's own regulation was involved in DNA methylation change. The purpose of this study is to detect DNA methylation landscape of miRNAs genes in mice liver fibrosis tissues. METHODS Male mice (10-12 weeks) were injected CCl4 from abdominal cavity to induced liver fibrosis. 850 K BeadChips were used to examine DNA methylation change in whole genome. The methylation change of 16 CpG dinucleotides located in promoter regions of 4 miRNA genes were detected by bisulfite sequencing polymerase chain reaction (BSP) to verify chip data accuracy, and these 4 miRNA genes' expressions were detected by RT-qPCR methods. RESULTS There are 769 differential methylation sites (DMS) in total between fibrotic liver tissue and normal mice liver tissue, which were related with 148 different miRNA genes. Chips array data were confirmed by bisulfite sequencing polymerase chain reaction (R = 0.953; P < 0.01). GO analysis of the target genes of 2 miRNA revealed that protein binding, cytoplasm and chromatin binding activity were commonly enriched; KEGG pathway enrichment analysis displayed that TGF-beta signaling pathway was commonly enriched. CONCLUSION The DNA of 148 miRNA genes was found to have methylation change in liver fibrosis tissue. These discoveries in miRNA genes are beneficial to future miRNA function research in liver fibrosis.
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Affiliation(s)
- Deming Li
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Wentong Yang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Jiaojiao Pang
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Guoying Yu
- State Key Laboratory of Cell Differentiation and Regulation, Henan International Joint Laboratory of Pulmonary Fibrosis, Henan Center for Outstanding Overseas Scientists of Pulmonary Fibrosis, Overseas Expertise Introduction Center for Discipline Innovation of Pulmonary Fibrosis (111 Project), College of Life Science, Henan Normal University, Xinxiang, Henan, China.
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Gibson D, Vo AH, Lambing H, Bhattacharya P, Tahir P, Chehab FF, Butowski N. A systematic review of high impact CpG sites and regions for MGMT methylation in glioblastoma [A systematic review of MGMT methylation in GBM]. BMC Neurol 2024; 24:103. [PMID: 38521933 PMCID: PMC10960428 DOI: 10.1186/s12883-024-03605-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/17/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND MGMT (O 6 -methylguanine-DNA methyltransferase) promoter methylation is a commonly assessed prognostic marker in glioblastoma (GBM). Epigenetic silencing of the MGMT gene by promoter methylation is associated with greater overall and progression free survival with alkylating agent regimens. To date, there is marked heterogeneity in how MGMT promoter methylation is tested and which CpG sites are interrogated. METHODS To further elucidate which MGMT promoter CpG sites are of greatest interest, we performed comprehensive searches in PubMed, Web of Science, and Embase and reviewed 2,925 article abstracts. We followed the GRADE scoring system to assess risk of bias and the quality of the studies we included. RESULTS We included articles on adult glioblastoma that examined significant sites or regions within MGMT promoter for the outcomes: overall survival, progression free survival, and/or MGMT expression. We excluded systemic reviews and articles on lower grade glioma. fifteen articles met inclusion criteria with variable overlap in laboratory and statistical methods employed, as well as CpG sites interrogated. Pyrosequencing or BeadChip arrays were the most popular methods utilized, and CpG sites between CpG's 70-90 were most frequently investigated. Overall, there was moderate concordance between the CpG sites that the studies reported to be highly predictive of prognosis. Combinations or means of sites between CpG's 73-89 were associated with improved OS and PFS. Six studies identified CpG sites associated with prognosis that were closer to the transcription start site: CpG's 8, 19, 22, 25, 27, 32,38, and CpG sites 21-37, as well as low methylation level of the enhancer regions. CONCLUSION The following systematic review details a comprehensive investigation of the current literature and highlights several potential key CpG sites that demonstrate significant association with OS, PFS, and MGMT expression. However, the relationship between extent of MGMT promoter methylation and survival may be non-linear and could be influenced by potential CpG hotspots, the extent of methylation at each CpG site, and MGMT enhancer methylation status. There were several limitations within the studies such as smaller sample sizes, variance between methylation testing methods, and differences in the various statistical methods to test for association to outcome. Further studies of high impact CpG sites in MGMT methylation is warranted.
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Affiliation(s)
- David Gibson
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA
- Department of Bioinformatics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Anh Huan Vo
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA.
| | - Hannah Lambing
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Prithanjan Bhattacharya
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA
| | - Peggy Tahir
- University of California, San Francisco Library, San Francisco, CA, USA
| | - Farid F Chehab
- Department of Laboratory Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas Butowski
- Department of Neuro-Oncology, University of California, San Francisco, 400 Parnassus Ave, San Francisco, CA, USA
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Zhang Z, Wang Q, Gao X, Tang X, Xu H, Wang W, Lei X. Reproductive toxicity of cadmium stress in male animals. Toxicology 2024:153787. [PMID: 38522818 DOI: 10.1016/j.tox.2024.153787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 03/26/2024]
Abstract
Cadmium (Cd) is a common heavy metal pollutant in the environment, and the widespread use of products containing Cd compounds in industry has led to excessive levels in the environment, which enter the animal body through the food chain, thus seriously affecting the reproductive development of animals. Related studies have reported that Cd severely affects spermatogonia development and spermatogenesis in animals. In contrast, the reproductive toxicity of Cd in males and its mechanism of action have not been clarified. Therefore, this paper reviewed the toxic effects of Cd on germ cells, spermatogonia somatic cells and hypothalamic-pituitary-gonadal axis (HPG axis) of male animals and its toxic action mechanisms of oxidative stress, apoptosis and autophagy from the perspectives of cytology, genetics and neuroendocrinology. The effects of Cd stress on epigenetic modification of reproductive development in male animals were also analyzed. We hope to provide a reference for the in-depth study of the toxicity of Cd on male animal reproduction.
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Affiliation(s)
- Zikun Zhang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China
| | - Qi Wang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China
| | - Xiaoge Gao
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China
| | - Xu Tang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China
| | - Huan Xu
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China
| | - Wenqiang Wang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China.
| | - Xin Lei
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi 716000, China; Yan'an Key Laboratory of Ecological Restoration, Yan'an, China.
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Lv L, Wei Q, Zhang J, Dong Y, Shan Z, Chang N, Zhao Y, Bian P, Yi Q. IGF2BP3 prevent HMGB1 mRNA decay in bladder cancer and development. Cell Mol Biol Lett 2024; 29:39. [PMID: 38504159 PMCID: PMC10949762 DOI: 10.1186/s11658-024-00545-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/05/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND IGF2BP3 functions as an RNA-binding protein (RBP) and plays a role in the posttranscriptional control of mRNA localization, stability, and translation. Its dysregulation is frequently associated with tumorigenesis across various cancer types. Nonetheless, our understanding of how the expression of the IGF2BP3 gene is regulated remains limited. The specific functions and underlying mechanisms of IGF2BP3, as well as the potential benefits of targeting it for therapeutic purposes in bladder cancer, are not yet well comprehended. METHODS The mRNA and protein expression were examined by RT-qPCR and western blotting, respectively. The methylation level of CpG sites was detected by Bisulfite sequencing PCR (BSP). The regulation of IGF2BP3 expression by miR-320a-3p was analyzed by luciferase reporter assay. The functional role of IGF2BP3 was determined through proliferation, colony formation, wound healing, invasion assays, and xenograft mouse model. The regulation of HMGB1 by IGF2BP3 was investigated by RNA immunoprecipitation (RIP) and mRNA stability assays. RESULTS We observed a significant elevation in IGF2BP3 levels within bladder cancer samples, correlating with more advanced stages and grades, as well as an unfavorable prognosis. Subsequent investigations revealed that the upregulation of IGF2BP3 expression is triggered by copy number gain/amplification and promoter hypomethylation in various tumor types, including bladder cancer. Furthermore, miR-320a-3p was identified as another negative regulator in bladder cancer. Functionally, the upregulation of IGF2BP3 expression exacerbated bladder cancer progression, including the proliferation, migration, and invasion of bladder cancer. Conversely, IGF2BP3 silencing produced the opposite effects. Moreover, IGF2BP3 expression positively correlated with inflammation and immune infiltration in bladder cancer. Mechanistically, IGF2BP3 enhanced mRNA stability and promoted the expression of HMGB1 by binding to its mRNA, which is a factor that promotes inflammation and orchestrates tumorigenesis in many cancers. Importantly, pharmacological inhibition of HMGB1 with glycyrrhizin, a specific HMGB1 inhibitor, effectively reversed the cancer-promoting effects of IGF2BP3 overexpression in bladder cancer. Furthermore, the relationship between HMGB1 mRNA and IGF2PB3 is also observed in mammalian embryonic development, with the expression of both genes gradually decreasing as embryonic development progresses. CONCLUSIONS Our present study sheds light on the genetic and epigenetic mechanisms governing IGF2BP3 expression, underscoring the critical involvement of the IGF2BP3-HMGB1 axis in driving bladder cancer progression. Additionally, it advocates for the investigation of inhibiting IGF2BP3-HMGB1 as a viable therapeutic approach for treating bladder cancer.
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Affiliation(s)
- Lei Lv
- Department of Cancer Epigenetics Program, Anhui Cancer Hospital, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, Anhui, China
| | - Qinqin Wei
- Institute of Radiation Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Jianxiao Zhang
- Medical Consulting Center, Hebei Children's Hospital, Shijiazhuang, 050030, Hebei, China
| | - Yitong Dong
- Institute of Radiation Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Zhenglei Shan
- The Second Clinical College, Anhui Medical University, Hefei, 230032, Anhui, China
| | - Na Chang
- Department of Radiation Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230031, Anhui, People's Republic of China
| | - Ye Zhao
- Institute of Radiation Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China.
| | - Po Bian
- Institute of Radiation Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China.
| | - Qiyi Yi
- Institute of Radiation Medicine, School of Basic Medical Sciences, Anhui Medical University, Hefei, 230032, Anhui, China.
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Karami Hezarcheshmeh F, Yaghmaei P, Hayati Roodbari N, Yari K. Methylation Status of cAMP-responsive Element Modulator (CREM) Gene in Infertile Men and Its Association with Sperm Parameters. Reprod Sci 2024:10.1007/s43032-024-01510-1. [PMID: 38499948 DOI: 10.1007/s43032-024-01510-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 03/01/2024] [Indexed: 03/20/2024]
Abstract
The methylation pattern of non-imprinting genes was little studied, although it is widely known that the abnormal methylation levels of imprinting genes are associated with different forms of male infertility. The purpose of this research was to assess the CREM gene's methylation status and seminal characteristics in infertile individuals who were potential intracytoplasmic sperm injection (ICSI) candidates. A total of 45 semen samples (15 normospermia, 15 asthenospermia, and 15 oligoasthenoteratospermia) were examined. Using aniline blue (AB) staining, we carried out conventional semen analysis, chromatin quality, and sperm maturity testing. DNA was taken from semen samples, and all isolated DNA was assessed using Nanodrop and gel electrophoresis. A quantitative methylation-specific polymerase chain reaction (Q-MSP) approach was used to quantify the methylation at the DMRs of the CREM gene. According to our findings, sperm count (P=0.012), concentration (P= 0.019), motility (P=0.006), progression (P=0.006), and normal morphology (P=0.004) were all inversely correlated with abnormal sperm chromatin condensation. Additionally, we noted that the methylation level of the CREM gene was considerably more significant in the oligoasthenoteratospermia group compared to the asthenospermia and normospermia groups (P<0.05). Additionally, sperm count (P=0.043), progression (P=0.026), and normal morphology (P=0.024) were all inversely linked with CREM methylation. Overall, the abnormal CREM methylation patterns have a negative impact on sperm parameters. Additionally, the CREM gene's DNA methylation status may serve as an epigenetic indicator of male infertility.
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Affiliation(s)
| | - Parichehreh Yaghmaei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Nasim Hayati Roodbari
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Kheirollah Yari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Andreiuolo F, Ferrone CK, Rajan S, Perry A, Guney E, Cham E, Giannini C, Toland A, Willard N, de Souza AS, Dazelle K, Chung HJ, Singh O, Conway K, Coley N, Dampier C, Abdullaev Z, Pratt D, Cimino PJ, Quezado M, Aldape K. Molecular and clinicopathologic characteristics of CNS embryonal tumors with BRD4::LEUTX fusion. Acta Neuropathol Commun 2024; 12:42. [PMID: 38500181 PMCID: PMC10946093 DOI: 10.1186/s40478-024-01746-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 02/19/2024] [Indexed: 03/20/2024] Open
Abstract
Central nervous system (CNS) embryonal tumors are a heterogeneous group of high-grade malignancies, and the increasing clinical use of methylation profiling and next-generation sequencing has led to the identification of molecularly distinct subtypes. One proposed tumor type, CNS tumor with BRD4::LEUTX fusion, has been described. As only a few CNS tumors with BRD4::LEUTX fusions have been described, we herein characterize a cohort of 9 such cases (4 new, 5 previously published) to further describe their clinicopathologic and molecular features. We demonstrate that CNS embryonal tumor with BRD4::LEUTX fusion comprises a well-defined methylation class/cluster. We find that patients are young (4 years or younger), with large tumors at variable locations, and frequently with evidence of leptomeningeal/cerebrospinal fluid (CSF) dissemination. Histologically, tumors were highly cellular with high-grade embryonal features. Immunohistochemically, 5/5 cases showed synaptophysin and 4/5 showed OLIG2 expression, thus overlapping with CNS neuroblastoma, FOXR2-activated. DNA copy number profiles were generally flat; however, two tumors had chromosome 1q gains. No recurring genomic changes, besides the presence of the fusion, were found. The LEUTX portion of the fusion transcript was constant in all cases assessed, while the BRD4 portion varied but included a domain with proto-oncogenic activity in all cases. Two patients with clinical follow up available had tumors with excellent response to chemotherapy. Two of our patients were alive without evidence of recurrence or progression after gross total resection and chemotherapy at 16 and 33 months. One patient relapsed, and the last of our four patients died of disease one month after diagnosis. Overall, this case series provides additional evidence for this as a distinct tumor type defined by the presence of a specific fusion as well as a distinct DNA methylation signature. Studies on larger series are required to further characterize these tumors.
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Affiliation(s)
- Felipe Andreiuolo
- Department of Pathology, Rede D'Or, Rio de Janeiro, RJ, Brazil
- D'Or Institute for Research and Education, Rio de Janeiro, RJ, Brazil
- Department of Pathology, Instituto Estadual Do Cérebro Paulo Niemeyer, Rio de Janeiro, RJ, Brazil
| | - Christina K Ferrone
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Sharika Rajan
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Arie Perry
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Ekin Guney
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Elaine Cham
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Caterina Giannini
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Angus Toland
- Department of Pathology, University of Colorado Hospital, Aurora, CO, USA
| | - Nicholas Willard
- Department of Pathology, University of Colorado Hospital, Aurora, CO, USA
| | | | - Karen Dazelle
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Hye-Jung Chung
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Omkar Singh
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Kyle Conway
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Nicholas Coley
- Diagnostic Pathology Medical Group, Inc., Sacramento, CA, USA
| | - Christopher Dampier
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Patrick J Cimino
- Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, USA
| | - Martha Quezado
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 10 Center Dr., Room 2S235, Bethesda, MD, 20892, USA.
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Yu B, Zheng B, Shen Y, Shen Y, Qiu H, Wu L, Chen Y, Cai X, Wu J, Hong Q. NLRC4 methylation and its response to intravenous immunoglobulin therapy in Kawasaki disease: a case control study. BMC Pediatr 2024; 24:190. [PMID: 38493129 PMCID: PMC10943762 DOI: 10.1186/s12887-024-04672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 02/25/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Kawasaki disease (KD) is a systemic vasculitis accompanied by many systemic physiological and biochemical changes. Elucidating its molecular mechanisms is crucial for diagnosing and developing effective treatments. NLR Family CARD Domain Containing 4 (NLRC4) encodes the key components of inflammasomes that function as pattern recognition receptors. The purpose of this study was to investigate the potential of NLRC4 methylation as a biomarker for KD. METHODS In this study, pyrosequencing was utilized to analyze NLRC4 promoter methylation in blood samples from 44 children with initial complete KD and 51 matched healthy controls. Methylation at five CpG sites within the NLRC4 promoter region was evaluated. RESULTS Compared to controls, NLRC4 methylation significantly decreased in KD patients (CpG1: p = 2.93E-06; CpG2: p = 2.35E-05; CpG3: p = 6.46E-06; CpG4: p = 2.47E-06; CpG5: p = 1.26E-05; average methylation: p = 5.42E-06). These changes were significantly reversed after intravenous immunoglobulin (IVIG) treatment. ROC curve analysis demonstrated remarkable diagnostic capability of mean NLRC4 gene methylation for KD (areas under ROC curve = 0.844, sensitivity = 0.75, p = 9.61E-06, 95% confidence intervals were 0.762-0.926 for mean NLRC4 methylation). In addition, NLRC4 promoter methylation was shown to be significantly negatively correlated with the levels of central granulocyte percentage, age, mean haemoglobin quantity and mean erythrocyte volume. Besides, NLRC4 promoter methylation was positively correlated with lymphocyte percentage, lymphocyte absolute value. CONCLUSIONS Our work revealed the role of peripheral NLRC4 hypomethylation in KD pathogenesis and IVIG treatment response, could potentially serve as a treatment monitoring biomarker, although its precise functions remain to be elucidated.
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Affiliation(s)
- Beirong Yu
- Department of Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, China
| | - Bangxu Zheng
- Department of Reproductive Medicine, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, China
| | - Yu Shen
- Department of Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, China
| | - Yijing Shen
- Department of Scientific Research, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, China
| | - Haiyan Qiu
- Department of Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, China
| | - Ling Wu
- Department of Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, China
| | - Yuanling Chen
- Department of Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, China
| | - Xiaohong Cai
- Medical School, Ningbo University, Ningbo, Zhejiang, China
| | - Junhua Wu
- Department of Pediatrics, Ningbo Women and Children's Hospital, Ningbo, Zhejiang, China.
| | - Qingxiao Hong
- Department of psychiatry, Affiliated Kangning Hospital of Ningbo University, Ningbo, 315201, Zhejiang, China.
- Key Laboratory of Addiction Research of Zhejiang Province, Ningbo Kangning Hospital, Ningbo, 315201, Zhejiang, China.
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Wang F, Hu D, Lou X, Wang L, Wang Y, Zhang T, Yan Z, Meng N, Lei Y, Zou Y. Predictive value of peripheral blood leukocytes-based methylation of Long non-coding RNA MALAT1 and H19 in the chemotherapy effect and prognosis of gastric cancer. Transl Oncol 2024; 44:101929. [PMID: 38493517 PMCID: PMC10958112 DOI: 10.1016/j.tranon.2024.101929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 05/27/2023] [Accepted: 03/05/2024] [Indexed: 03/19/2024] Open
Abstract
BACKGROUND The predictive value of the methylation of Long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and H19 promoters in peripheral blood leukocytes as a non-invasive biomarker for the chemotherapy effect and prognosis gastric cancer (GC) is unclear. METHODS The DNA methylation of H19 and MALAT1 between chemotherapy-sensitive and non-sensitive groups and between groups with better and worse survival of GC was compared using regression analyses. Several predictive nomograms were constructed. The genetic alteration of MALAT1 and H19 and the association between gene expression and immune status in GC were also investigated using bioinformatics analysis. RESULTS Higher genetic methylations in peripheral blood were noticed in GC groups with poorer survival. The constructed nomograms presented strong predictive values for the chemotherapy effect and 3-year survival of disease-free survival, progression-free survival, and overall survival, with the area under the curve as 0.838, 0.838, 0.912, and 0.925, respectively. Significant correlations between MALAT1 or H19 expression and marker genes of immune checkpoints and immune pathways were noticed. The high infiltration of macrophages in H19-high and low infiltration of CD8+ T cells in MALAT1-high groups were associated with worse survival of GC. CONCLUSIONS MALAT1 and H19 have the potential to predict the chemotherapy response and clinical outcomes of GC.
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Affiliation(s)
- Fang Wang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China.
| | - Dingtao Hu
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai 200433, PR China
| | - Xiaoqi Lou
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Linlin Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Yuhua Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Tingyu Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Ziye Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
| | - Nana Meng
- Department of Quality Management Office, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Yu Lei
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, PR China
| | - Yanfeng Zou
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, PR China
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Cui J, Li L, Wei S, Wei Y, Gong Y, Yan H, Yu Y, Lin X, Qin H, Li G, Yi L. Involvement of GSTP1 in low dose radiation-induced apoptosis in GM12878 cells. Ecotoxicol Environ Saf 2024; 273:116128. [PMID: 38387144 DOI: 10.1016/j.ecoenv.2024.116128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 02/24/2024]
Abstract
BACKGROUND Low-dose ionizing radiation-induced protection and damage are of great significance among radiation workers. We aimed to study the role of glutathione S-transferase Pi (GSTP1) in low-dose ionizing radiation damage and clarify the impact of ionizing radiation on the biological activities of cells. RESULTS In this study, we collected peripheral blood samples from healthy adults and workers engaged in radiation and radiotherapy and detected the expression of GSTP1 by qPCR. We utilized γ-rays emitted from uranium tailings as a radiation source, with a dose rate of 14 μGy/h. GM12878 cells subjected to this radiation for 7, 14, 21, and 28 days received total doses of 2.4, 4.7, 7.1, and 9.4 mGy, respectively. Subsequent analyses, including flow cytometry, MTS, and other assays, were performed to assess the ionizing radiation's effects on cellular biological functions. In peripheral blood samples collected from healthy adults and radiologic technologist working in a hospital, we observed a decreased expression of GSTP1 mRNA in radiation personnel compared to the healthy controls. In cultured GM12878 cells exposed to low-dose ionizing radiation from uranium tailings, we noted significant changes in cell morphology, suppression of proliferation, delay in cell cycle progression, and increased apoptosis. These effects were partially reversed by overexpression of GSTP1. Moreover, low-dose ionizing radiation increased GSTP1 gene methylation and downregulated GSTP1 expression. Furthermore, low-dose ionizing radiation affected the expression of GSTP1-related signaling molecules. CONCLUSIONS This study shows that low-dose ionizing radiation damages GM12878 cells and affects their proliferation, cell cycle progression, and apoptosis. In addition, GSTP1 plays a modulating role under low-dose ionizing radiation damage conditions. Low-dose ionizing radiation affects the expression of Nrf2, JNK, and other signaling molecules through GSTP1.
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Affiliation(s)
- Jian Cui
- Institute of Cytology and Genetics, The Hengyang Key Laboratory of Cellular Stress Biology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, The First Affiliated Hospital, Institute of Cardiovascular Disease, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Linwei Li
- Institute of Cytology and Genetics, The Hengyang Key Laboratory of Cellular Stress Biology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, The First Affiliated Hospital, Institute of Cardiovascular Disease, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Shuang Wei
- Institute of Cytology and Genetics, The Hengyang Key Laboratory of Cellular Stress Biology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, The First Affiliated Hospital, Institute of Cardiovascular Disease, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Yuanyun Wei
- Institute of Cytology and Genetics, The Hengyang Key Laboratory of Cellular Stress Biology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, The First Affiliated Hospital, Institute of Cardiovascular Disease, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Yaqi Gong
- Institute of Cytology and Genetics, The Hengyang Key Laboratory of Cellular Stress Biology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, The First Affiliated Hospital, Institute of Cardiovascular Disease, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Hongxia Yan
- Institute of Cytology and Genetics, The Hengyang Key Laboratory of Cellular Stress Biology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, The First Affiliated Hospital, Institute of Cardiovascular Disease, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Yueqiu Yu
- Institute of Cytology and Genetics, The Hengyang Key Laboratory of Cellular Stress Biology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, The First Affiliated Hospital, Institute of Cardiovascular Disease, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Xiang Lin
- Institute of Cytology and Genetics, The Hengyang Key Laboratory of Cellular Stress Biology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, The First Affiliated Hospital, Institute of Cardiovascular Disease, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Hui Qin
- Institute of Cytology and Genetics, The Hengyang Key Laboratory of Cellular Stress Biology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, The First Affiliated Hospital, Institute of Cardiovascular Disease, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Guoqing Li
- Institute of Cytology and Genetics, The Hengyang Key Laboratory of Cellular Stress Biology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, The First Affiliated Hospital, Institute of Cardiovascular Disease, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China
| | - Lan Yi
- Institute of Cytology and Genetics, The Hengyang Key Laboratory of Cellular Stress Biology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, The First Affiliated Hospital, Institute of Cardiovascular Disease, The Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
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La-Ongthong K, Chantarojsiri T, Soorukram D, Leowanawat P, Reutrakul V, Kuhakarn C. Electro-oxidative Methylation of 2-Isocyanobiaryls Using N,N-dimethylformamide (DMF) as Carbon Source: Synthesis of 6-Methylphenanthridines. Chem Asian J 2024:e202400176. [PMID: 38489229 DOI: 10.1002/asia.202400176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/14/2024] [Accepted: 03/14/2024] [Indexed: 03/17/2024]
Abstract
A benign electrochemical method to access 6-methylphenanthridines from 2-isocyanobiaryls using N,N-dimethylformamide (DMF) as a methyl source is reported. The protocol operates at ambient temperature without the need for harmful methylating reagents. Mechanistic studies suggested that DMF delivered a methylene synthon, followed by reduction at the cathode and tautomerization. The method offers environmental benefits by avoiding metal-based reagents and harsh conditions.
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Affiliation(s)
- Kannika La-Ongthong
- Department of Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Teera Chantarojsiri
- Department of Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Darunee Soorukram
- Department of Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Pawaret Leowanawat
- Department of Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Vichai Reutrakul
- Department of Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
| | - Chutima Kuhakarn
- Department of Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
- Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand
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Duan C, Yan Z, Wu C, Zhou X, Bao W. DNA methylation characteristics associated with chemotherapy resistance in epithelial ovarian cancer. Heliyon 2024; 10:e27212. [PMID: 38468944 PMCID: PMC10926131 DOI: 10.1016/j.heliyon.2024.e27212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Objective The high mortality rate of epithelial ovarian cancer (EOC) is often attributed to the frequent development of chemoresistance. DNA methylation is a predictive biomarker for chemoresistance. Methods This study utilized DNA methylation profiles and relevant information from GEO and TCGA to identify different methylated CpG sites (DMCs) between chemoresistant and chemosensitive patients. Subsequently, we constructed chemoresistance risk models with DMCs. The genes corresponding to candidate DMCs in chemoresistance risk models were further analyzed to identify different methylated gene symbols (DMGs) associated with chemoresistance. The DMGs that showed a strong correlation with the corresponding DMCs were analyzed through immunohistochemistry. Results Compared to chemosensitive EOC patients, chemoresistant patients showed 423 hypermethylated CpGs and 1445 hypomethylated CpGs. The chemoresistance risk models based on DMCs have shown the improved predictive ability for chemoresistance in EOC (AUC = 65.0-76.2%). The methylations of cg25510164, cg13154880, cg15362155 and cg08665359 were strongly associated with decreased risk of chemoresistance. Conversely, the methylation of cg08872590 and cg14739437 significantly increased the risk. We identified 13 DMGs, from 47 DMCs corresponding genes, between chemosensitive and chemoresistant samples. Among the DMGs, the expression levels of DDR2 and OPCML exhibited strong correlations with the corresponding DMCs. DDR2 and OPCML both showed enhanced expression in chemoresistant ovarian microarray tissue. Conclusions Hypomethylated CpGs may play a significant role in DNA methylation associated with chemoresistance in EOC. The epigenetic modification of DDR2 could have important implications for the development of chemoresistance. Our study provides valuable insights for future research on DNA methylation in the chemoresistance of EOC.
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Affiliation(s)
| | | | - Cailiang Wu
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Xuexin Zhou
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
| | - Wei Bao
- Department of Obstetrics and Gynecology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200080, Shanghai, China
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Wittwer CT, Hemmert AC, Kent JO, Rejali NA. DNA melting analysis. Mol Aspects Med 2024; 97:101268. [PMID: 38489863 DOI: 10.1016/j.mam.2024.101268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 02/19/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
Melting is a fundamental property of DNA that can be monitored by absorbance or fluorescence. PCR conveniently produces enough DNA to be directly monitored on real-time instruments with fluorescently labeled probes or dyes. Dyes monitor the entire PCR product, while probes focus on a specific locus within the amplicon. Advances in amplicon melting include high resolution instruments, saturating DNA dyes that better reveal multiple products, prediction programs for domain melting, barcode taxonomic identification, high speed microfluidic melting, and highly parallel digital melting. Most single base variants and small insertions or deletions can be genotyped by high resolution amplicon melting. High resolution melting also enables heterozygote scanning for any variant within a PCR product. A web application (uMelt, http://www.dna-utah.org) predicts amplicon melting curves with multiple domains, a useful tool for verifying intended products. Additional applications include methylation assessment, copy number determination and verification of sequence identity. When amplicon melting does not provide sufficient detail, unlabeled probes or snapback primers can be used instead of covalently labeled probes. DNA melting is a simple, inexpensive, and powerful tool with many research applications that is beginning to make its mark in clinical diagnostics.
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Affiliation(s)
- Carl T Wittwer
- Department of Pathology, University of Utah, Salt Lake City, UT, USA.
| | | | - Jana O Kent
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
| | - Nick A Rejali
- Department of Pathology, University of Utah, Salt Lake City, UT, USA
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Wang F, Hu D, Lou X, Wang Y, Wang L, Zhang T, Yan Z, Meng N, Zou Y. BNIP3 and DAPK1 methylation in peripheral blood leucocytes are noninvasive biomarkers for gastric cancer. Gene 2024; 898:148109. [PMID: 38142898 DOI: 10.1016/j.gene.2023.148109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 12/26/2023]
Abstract
OBJECTIVE The objective of this study is to comprehensively investigate the potential value of BNIP3 and DAPK1 methylation in peripheral blood leukocytes as a non-invasive biomarker for the detection of gastric cancer (GC), prediction of chemotherapy efficacy, and prognosis assessment. PATIENTS AND METHODS Initially, multiple bioinformatic analyses were employed to explore the genetic landscape and biological effects of BNIP3 and DAPK1 in GC tissues. Subsequently, case-control and prospective follow-up studies were conducted to compare the differences in BNIP3 and DAPK1 methylation levels in peripheral blood leukocytes among GC patients and healthy controls, as well as between patients exhibiting sensitivity and resistance to platinum plus fluorouracil treatment, and between patients with varying survival outcomes of GC. Additionally, several predictive nomograms were constructed based on the identified CpG sites and relevant clinical parameters to forecast the occurrence of GC, chemotherapy efficacy, and prognosis. RESULTS The upregulation of BNIP3 and DAPK1 was found to be associated with the development and poorer survival outcomes of GC. Furthermore, the expression of BNIP3/DAPK1 exhibited an inverse relationship with their DNA methylation levels and demonstrated a positive correlation with immune cell infiltration, as well as the IC50 values of 5-Fluorouracil and Cisplatin in GC tissues. Increased infiltration of macrophages in the high-expression groups was observed to be linked to unfavorable GC survival. In the case-control and follow-up studies, lower methylation levels of BNIP3 and DAPK1 were identified in the peripheral leukocytes of GC patients compared to healthy controls. Hypomethylation was also associated with more aggressive subtypes, diminished chemotherapy efficacy, and poorer survival outcomes in GC. CONCLUSION The DNA methylation of BNIP3 and DAPK1 in peripheral blood leukocytes holds promise as a novel non-invasive biomarker for predicting the occurrence of GC, chemotherapy efficacy, and prognosis assessment.
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Affiliation(s)
- Fang Wang
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
| | - Dingtao Hu
- Clinical Cancer Institute, Center for Translational Medicine, Naval Medical University, Shanghai 2004332, China
| | - Xiaoqi Lou
- Department of Oncology, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yuhua Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Linlin Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Tingyu Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Ziye Yan
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
| | - Nana Meng
- Department of Quality Management Office, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Yanfeng Zou
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, Anhui, China
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Langford N, Fargeot L, Blanchet S. Spatial covariation between genetic and epigenetic diversity in wild plant and animal populations: a meta-analysis. J Exp Biol 2024; 227:jeb246009. [PMID: 38449323 DOI: 10.1242/jeb.246009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Epigenetic variation may be crucial in understanding the structure of wild populations, thereby aiding in their management and conservation. However, the relationship between epigenetic and genetic variation remains poorly understood, especially in wild populations. To address this, we conducted a meta-analysis of studies that examined the genetic and epigenetic structures of wild plant and animal populations. We aimed to determine whether epigenetic variation is spatially independent of genetic variation in the wild and to highlight the conditions under which epigenetic variation might be informative. We show a significant positive correlation between genetic and epigenetic pairwise differentiation, indicating that in wild populations, epigenetic diversity is closely linked to genetic differentiation. The correlation was weaker for population pairs that were weakly differentiated genetically, suggesting that in such cases, epigenetic marks might be independent of genetic marks. Additionally, we found that global levels of genetic and epigenetic differentiation were similar across plant and animal populations, except when populations were weakly differentiated genetically. In such cases, epigenetic differentiation was either higher or lower than genetic differentiation. Our results suggest that epigenetic information is particularly relevant in populations that have recently diverged genetically or are connected by gene flow. Future studies should consider the genetic structure of populations when inferring the role of epigenetic diversity in local adaptation in wild populations. Furthermore, there is a need to identify the factors that sustain the links between genetic and epigenetic diversity to improve our understanding of the interplay between these two forms of variation in wild populations.
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Affiliation(s)
- Nadia Langford
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200 Moulis, France
| | - Laura Fargeot
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200 Moulis, France
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Université Paul Sabatier (UPS); Station d'Ecologie Théorique et Expérimentale, UAR 2029, F-09200 Moulis, France
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Ehret F, Zühlke O, Schweizer L, Kahn J, Csapo-Schmidt C, Roohani S, Zips D, Capper D, Adeberg S, Abdollahi A, Knoll M, Kaul D. Validation of a methylation-based signature for subventricular zone involvement in glioblastoma. J Neurooncol 2024; 167:89-97. [PMID: 38376766 PMCID: PMC10978677 DOI: 10.1007/s11060-024-04570-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/11/2024] [Indexed: 02/21/2024]
Abstract
PURPOSE Glioblastomas (GBM) with subventricular zone (SVZ) contact have previously been associated with a specific epigenetic fingerprint. We aim to validate a reported bulk methylation signature to determine SVZ contact. METHODS Methylation array analysis was performed on IDHwt GBM patients treated at our institution. The v11b4 classifier was used to ensure the inclusion of only receptor tyrosine kinase (RTK) I, II, and mesenchymal (MES) subtypes. Methylation-based assignment (SVZM ±) was performed using hierarchical cluster analysis. Magnetic resonance imaging (MRI) (T1ce) was independently reviewed for SVZ contact by three experienced readers. RESULTS Sixty-five of 70 samples were classified as RTK I, II, and MES. Full T1ce MRI-based rater consensus was observed in 54 cases, which were retained for further analysis. Epigenetic SVZM classification and SVZ were strongly associated (OR: 15.0, p = 0.003). Thirteen of fourteen differential CpGs were located in the previously described differentially methylated LRBA/MAB21L2 locus. SVZ + tumors were linked to shorter OS (hazard ratio (HR): 3.80, p = 0.02) than SVZM + at earlier time points (time-dependency of SVZM, p < 0.05). Considering the SVZ consensus as the ground truth, SVZM classification yields a sensitivity of 96.6%, specificity of 36.0%, positive predictive value (PPV) of 63.6%, and negative predictive value (NPV) of 90.0%. CONCLUSION Herein, we validated the specific epigenetic signature in GBM in the vicinity of the SVZ and highlighted the importance of methylation of a part of the LRBA/MAB21L2 gene locus. Whether SVZM can replace MRI-based SVZ assignment as a prognostic and diagnostic tool will require prospective studies of large, homogeneous cohorts.
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Affiliation(s)
- Felix Ehret
- Department of Radiation Oncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Oliver Zühlke
- Department of Radiation Oncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Leonille Schweizer
- Institute of Neurology (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany
| | - Johannes Kahn
- Department of Radiology, Health and Medical University, Potsdam, Germany
| | - Christoph Csapo-Schmidt
- Department of Neuroradiology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Siyer Roohani
- Department of Radiation Oncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charité Junior Clinician Scientist Program, Berlin, Germany
| | - Daniel Zips
- Department of Radiation Oncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
- Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David Capper
- Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany
| | - Sebastian Adeberg
- Department of Radiation Oncology, University Hospital Marburg/Gießen, Marburg, Germany
| | - Amir Abdollahi
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Maximilian Knoll
- Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - David Kaul
- Department of Radiation Oncology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität Zu Berlin, Berlin, Germany.
- Charité - Universitätsmedizin Berlin, Berlin, Germany; German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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Casali C, Galgano L, Zannino L, Siciliani S, Cavallo M, Mazzini G, Biggiogera M. Impact of heat and cold shock on epigenetics and chromatin structure. Eur J Cell Biol 2024; 103:151373. [PMID: 38016352 DOI: 10.1016/j.ejcb.2023.151373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 11/01/2023] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
Cells are continuously exposed to various sources of insults, among which temperature variations are extremely common. Epigenetic mechanisms, critical players in gene expression regulation, undergo alterations due to these stressors, potentially leading to health issues. Despite the significance of DNA methylation and histone modifications in gene expression regulation, their changes following heat and cold shock in human cells remain poorly understood. In this study, we investigated the epigenetic profiles of human cells subjected to hyperthermia and hypothermia, revealing significant variations. Heat shock primarily led to DNA methylation increments and epigenetic modifications associated with gene expression silencing. In contrast, cold shock presented a complex scenario, with both methylation and demethylation levels increasing, indicating different epigenetic responses to the opposite thermal stresses. These temperature-induced alterations in the epigenome, particularly their impact on chromatin structural organization, represent an understudied area that could offer important insights into genome function and potential prospects for therapeutic targets.
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Affiliation(s)
- Claudio Casali
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy.
| | - Luca Galgano
- Laboratory of Biochemistry, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Lorena Zannino
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Stella Siciliani
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Margherita Cavallo
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | | | - Marco Biggiogera
- Laboratory of Cell Biology and Neurobiology, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
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Jiang Y, Chen J, Guo L, Lan Y, Li G, Liu Q, Li H, Deng F, Guo X, Wu S. Short-term effects of ambient gaseous air pollution on blood platelet mitochondrial DNA methylation and myocardial ischemia. Environ Int 2024; 185:108533. [PMID: 38430585 DOI: 10.1016/j.envint.2024.108533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/14/2024] [Accepted: 02/23/2024] [Indexed: 03/04/2024]
Abstract
BACKGROUND The potential effects of short-term exposure to major ambient gaseous pollutants (ozone: O3, carbon monoxide: CO, and sulfur dioxide: SO2) on platelet mitochondrial DNA (mtDNA) methylation have been uncertain and no studies have examined whether platelet mtDNA methylation levels could modify the associations between ambient gaseous pollutants and the risks of ST-segment depression (STDE) and T-wave inversion events (TIE), two indicators of myocardial ischemia. METHODS This study used data from a randomized, double-blind, placebo-controlled intervention study with a standardized 24-hour exposure protocol among 110 participants in Beijing. Absolute changes in platelet mtDNA methylation (ACmtDNAm) levels were determined by two repeated measurements on platelet mtDNA methylation levels in blood samples collected before and after the 24-hour exposure period. A multivariable linear regression model and a generalized linear model with a Poisson link function were used to investigate the associations of ambient gaseous pollutants with platelet mtDNA methylation levels, STDE, and TIE, respectively. RESULTS Short-term O3 exposure was significantly associated with decreased ACmtDNAm at ATP6_P1 but increased ACmtDNAm at mt12sRNA, MT-COX1, and MT-COX1_P2; short-term CO and SO2 exposures were significantly associated with decreased ACmtDNAm at D-loop, MT-COX3- and ATP-related genes. Moreover, short-term O3 exposure was significantly associated with increased risks of STDE and TIE, and ACmtDNAm at MT-COX1 and MT-COX1_P2 modified the association between short-term O3 exposure and STDE events. L-Arg supplementation attenuated the effects of ambient gaseous pollutants, particularly O3, on ACmtDNAm and STDE. CONCLUSIONS Platelet mtDNA methylation levels are promising biomarkers of short-term exposure to ambient gaseous air pollution, and are likely implicated in the mechanism behind the association of ambient O3 pollution with adverse cardiovascular effects. L-Arg supplementation showed the potential to mitigate the adverse effects of ambient O3 pollution.
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Affiliation(s)
- Yunxing Jiang
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China; Key Laboratory of Trace Elements and Endemic Diseases in Ministry of Health, Xi'an, Shaanxi, China; Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, Shaanxi, China
| | - Juan Chen
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China; Key Laboratory of Trace Elements and Endemic Diseases in Ministry of Health, Xi'an, Shaanxi, China; Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, Shaanxi, China
| | - Liqiong Guo
- Institute of Disaster and Emergency Medicine, Tianjin University, Tianjin, China; Wenzhou Safety (Emergency) Institute, Tianjin University, Wenzhou, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin, China
| | - Yang Lan
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China; Key Laboratory of Trace Elements and Endemic Diseases in Ministry of Health, Xi'an, Shaanxi, China; Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, Shaanxi, China
| | - Ge Li
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China; Shaanxi Provincial Institute for Endemic Disease Control, Xi'an, Shaanxi, China
| | - Qisijing Liu
- Research Institute of Public Health, School of Medicine, Nankai University, Tianjin, China
| | - Hongyu Li
- Department of Scientific Research, Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Furong Deng
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, China
| | - Xinbiao Guo
- Department of Occupational and Environmental Health Sciences, School of Public Health, Peking University, Beijing, China
| | - Shaowei Wu
- Department of Occupational and Environmental Health, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi, China; Key Laboratory of Environment and Genes Related to Diseases, Ministry of Education, Xi'an, Shaanxi, China; Key Laboratory of Trace Elements and Endemic Diseases in Ministry of Health, Xi'an, Shaanxi, China; Key Laboratory for Disease Prevention and Control and Health Promotion of Shaanxi Province, Xi'an, Shaanxi, China.
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Lee JE, Park SU, So MH, Lee HY. Age prediction using DNA methylation of Y-chromosomal CpGs in semen samples. Forensic Sci Int Genet 2024; 69:103007. [PMID: 38217952 DOI: 10.1016/j.fsigen.2024.103007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 12/29/2023] [Accepted: 01/03/2024] [Indexed: 01/15/2024]
Abstract
In cases of sexual assault, the evidence often exists as a mixture of female and male body fluids, and in many cases, contains a higher proportion of female body fluids than males. In these cases, Y-STR, rather than autosomal STRs, can provide useful information. It becomes very difficult to identify the true suspect if there is no match among known suspects or if a match exists for two or more suspects, e.g. two suspects from the same paternal lineage. However, age prediction using the DNA methylation of Y-chromosomal CpGs can help narrow the search for unknown suspects and discriminate between older and younger suspects. Therefore, the DNA methylation profiles of semen samples from 56 healthy Korean males were generated using Illumina's Infinium MethylationEPIC BeadChip Array. Among the ten identified age-associated CpG markers located in the Y-chromosome, nine were used to construct age prediction models. The identified markers were further investigated in the MPS analysis of 147 semen samples, and the multiplex assay was validated with the reliability, reproducibility and sensitivity tests. Several age prediction models were constructed using the MPS data with the multiple linear regression, stepwise linear regression, ridge linear regression, lasso regression, elastic net linear regression and support vector machine analyses, and all showed MAEs of 5 to 7 years in the test set samples. Six single-source female samples were also subjected to MPS analysis but showed very low coverage that could not affect the analysis of the mixed samples. Therefore, the age prediction models of the present study are expected to provide useful investigative leads, especially in mixed male and female samples from sexual assault cases.
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Affiliation(s)
- Ji Eun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, the Republic of Korea
| | - Sang Un Park
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, the Republic of Korea
| | - Moon Hyun So
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, the Republic of Korea
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, the Republic of Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, the Republic of Korea.
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Xin W, Tu S, Yi S, Xiong Y, Fang K, Sun G, Xiao W. Clinical significance of tumor suppressor genes methylation in circulating tumor DNA of patients with pancreatic cancer. Gene 2024; 897:148078. [PMID: 38097094 DOI: 10.1016/j.gene.2023.148078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/14/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023]
Abstract
BACKGROUND Circulating tumor DNA (ctDNA) has emerged as a potential diagnostic and prognostic biomarker in various tumors. However, the role of tumor suppressor genes (TSGs) methylation in ctDNA of patients with pancreatic cancer (PC) remains largely unclear. METHODS Patients with PC (n = 43), pancreatic benign diseases (n = 39), and healthy controls (n = 20) were enrolled in the study. Quantitative analysis of methylation pattern of five candidate TSGs including NPTX2, RASSF1A, EYA2, p16, and ppENK in ctDNA was performed by next generation sequencing (NGS). The diagnostic performances of these 5-TSGs methylation were assessed by the operating characteristic (ROC) curve and clinicopathological features correlation analysis. Meanwhile, the changes in methylation levels of these 5-TSGs on the 7th postoperative day were evaluated in 23 PC patients who underwent radical resection. RESULTS The methylation levels of RASSF1A, EYA2, ppENK and p16 genes in patients with PC were significantly higher than those in healthy controls. EYA2, p16 and ppENK genes showed significantly hypermethylation in PC than those in pancreatic benign diseases. NPTX2, RASSF1A, EYA2, p16 and ppENK genes showed significantly hypermethylation in pancreatic benign diseases than those in healthy controls (P < 0.05). The methylation levels of these 5 candidate TSGs were not correlated with the tumor size, nerve invasion, lymph node metastasis and TNM stage of PC. The AUC of these biomarkers for diagnosis of PC ranged from 0.65 to 0.96. The AUC values of these methylated genes and CpG sites for differentiating malignant and benign pancreatic diseases were ranging from 0.68 to 0.92. Combined the hypermethylated genes improved the detective ability of PC than single gene. The methylation levels of NPTX2, EYA2 and ppENK genes were significantly decreased after radical resection of PC. CONCLUSION Quantitative analysis of methylation pattern of NPTX2, RASSF1A, EYA2, p16 and ppENK in ctDNA by NGS could be a valuable non-invasive tool for detection and monitoring of PC.
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Affiliation(s)
- WanPeng Xin
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Shuju Tu
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Siqing Yi
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Yuanpeng Xiong
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Kang Fang
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Gen Sun
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Weidong Xiao
- Department of General Surgery, The First Affiliated Hospital, Nanchang University, Nanchang, Jiangxi, China; Institute of Digestive Surgery, Nanchang University, Nanchang, Jiangxi, China.
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Hobble HV, Schaner Tooley CE. Intrafamily heterooligomerization as an emerging mechanism of methyltransferase regulation. Epigenetics Chromatin 2024; 17:5. [PMID: 38429855 PMCID: PMC10908127 DOI: 10.1186/s13072-024-00530-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/10/2024] [Indexed: 03/03/2024] Open
Abstract
Protein and nucleic acid methylation are important biochemical modifications. In addition to their well-established roles in gene regulation, they also regulate cell signaling, metabolism, and translation. Despite this high biological relevance, little is known about the general regulation of methyltransferase function. Methyltransferases are divided into superfamilies based on structural similarities and further classified into smaller families based on sequence/domain/target similarity. While members within superfamilies differ in substrate specificity, their structurally similar active sites indicate a potential for shared modes of regulation. Growing evidence from one superfamily suggests a common regulatory mode may be through heterooligomerization with other family members. Here, we describe examples of methyltransferase regulation through intrafamily heterooligomerization and discuss how this can be exploited for therapeutic use.
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Affiliation(s)
- Haley V Hobble
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, 14203, USA
| | - Christine E Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, 14203, USA.
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