1
|
Liu L, Zou C, Shen J, Huang R, Zhang F, Du Y, Luo X, Yang A, Zhang J, Guan Y, Yan X. MUL1 identified as mitochondria-linked biomarker promoting cisplatin resistance in OC cells. Gene 2024; 930:148841. [PMID: 39134101 DOI: 10.1016/j.gene.2024.148841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 07/22/2024] [Accepted: 08/09/2024] [Indexed: 08/17/2024]
Abstract
Ovarian cancer (OC) ranks among the prevalent tumors affecting the female reproductive system. The aim of this study was to evaluate mitochondria-associated platinum resistance genes using organoid models. Univariate Cox regression, LASSO and multivariate Cox regression analyses were performed on The Cancer Genome Atlas (TCGA) database to construct 2-gene prognostic signature (MUL1 and SSBP1), and GSE26712 dataset was used for external validation. In addition, the relationship between MUL1 and platinum resistance was examined by organoid culture, lentiviral transduction, CCK8 assay, and Western blot. The results showed that patients in the high-risk group exhibited significantly worse OS (P = 0.002, P = 0.017). Drug sensitivity analysis revealed that platinum resistance increased with the upregulation of MUL1 expression (Cor = 0.5154, P = 0.02). Our experimental findings demonstrated that knockout of the MUL1 gene significantly increased apoptosis and enhanced the sensitivity of the OC cell line A2780 to cisplatin. Through this study, we have provided strong evidence for further research on prognostic risk factors and individualized treatment in OC patients, and provided new insights into addressing platinum resistance in OC.
Collapse
Affiliation(s)
- Lixiao Liu
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China.
| | - Chengyang Zou
- The Affiliated Central Hospital of Lishui, The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui Hospital of Zhejiang University, Lishui 323000, China.
| | - Jingtian Shen
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Rong Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Fubin Zhang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China.
| | - Yongming Du
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China.
| | - Xishao Luo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Aiwu Yang
- Department of Obstetrics and Gynecology, The Wenzhou People's Hospital, Wenzhou, Zhejiang, China.
| | - Jinsan Zhang
- Department of Medical Research Center and the Department of Pulmonary Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| | - Yutao Guan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China.
| | - Xiaojian Yan
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, China.
| |
Collapse
|
2
|
Dwivedi R, Kaushik M, Tripathi M, Dada R, Tiwari P. Unraveling the genetic basis of epilepsy: Recent advances and implications for diagnosis and treatment. Brain Res 2024; 1843:149120. [PMID: 39032529 DOI: 10.1016/j.brainres.2024.149120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/05/2024] [Accepted: 07/08/2024] [Indexed: 07/23/2024]
Abstract
Epilepsy, affecting approximately 1% of the global population, manifests as recurring seizures and is heavily influenced by genetic factors. Recent advancements in genetic technologies have revolutionized our understanding of epilepsy's genetic landscape. Key studies, such as the discovery of mutations in ion channels (e.g., SCN1A and SCN2A), neurotransmitter receptors (e.g., GABRA1), and synaptic proteins (e.g., SYNGAP1, KCNQ2), have illuminated critical pathways underlying epilepsy susceptibility and pathogenesis. Genome-wide association studies (GWAS) have identified specific genetic variations linked to epilepsy risk, such as variants near SCN1A and PCDH7, enhancing diagnostic accuracy and enabling personalized treatment strategies. Moreover, epigenetic mechanisms, including DNA methylation (e.g., MBD5), histone modifications (e.g., HDACs), and non-coding RNAs (e.g., miR-134), play pivotal roles in altering gene expression and synaptic plasticity, contributing to epileptogenesis. These discoveries offer promising avenues for therapeutic interventions aimed at improving outcomes for epilepsy patients. Genetic testing has become essential in clinical practice, facilitating precise diagnosis and tailored management approaches based on individual genetic profiles. Furthermore, insights into epigenetic regulation suggest novel therapeutic targets for developing more effective epilepsy treatments. In summary, this review highlights significant progress in understanding the genetic and epigenetic foundations of epilepsy. By integrating findings from key studies and specifying genes involved in epigenetic modifications, we underscore the potential for advanced therapeutic strategies in this complex neurological disorder, emphasizing the importance of personalized medicine approaches in epilepsy management.
Collapse
Affiliation(s)
- Rekha Dwivedi
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Meenakshi Kaushik
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Manjari Tripathi
- Department of Neurology, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Rima Dada
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India
| | - Prabhakar Tiwari
- Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 110029, India.
| |
Collapse
|
3
|
Hinton AO, Vue Z, Scudese E, Neikirk K, Kirabo A, Montano M. Mitochondrial heterogeneity and crosstalk in aging: Time for a paradigm shift? Aging Cell 2024; 23:e14296. [PMID: 39188058 PMCID: PMC11464123 DOI: 10.1111/acel.14296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/24/2024] [Accepted: 07/26/2024] [Indexed: 08/28/2024] Open
Abstract
The hallmarks of aging have been influential in guiding the biology of aging research, with more recent and growing recognition of the interdependence of these hallmarks on age-related health outcomes. However, a current challenge is personalizing aging trajectories to promote healthy aging, given the diversity of genotypes and lived experience. We suggest that incorporating heterogeneity-including intrinsic (e.g., genetic and structural) and extrinsic (e.g., environmental and exposome) factors and their interdependence of hallmarks-may move the dial. This editorial perspective will focus on one hallmark, namely mitochondrial dysfunction, to exemplify how consideration of heterogeneity and interdependence or crosstalk may reveal new perspectives and opportunities for personalizing aging research. To this end, we highlight heterogeneity within mitochondria as a model.
Collapse
Affiliation(s)
- Antentor O. Hinton
- Department of Molecular Physiology and BiophysicsVanderbilt UniversityNashvilleTennesseeUSA
| | - Zer Vue
- Department of Molecular Physiology and BiophysicsVanderbilt UniversityNashvilleTennesseeUSA
| | - Estevão Scudese
- Department of Molecular Physiology and BiophysicsVanderbilt UniversityNashvilleTennesseeUSA
| | - Kit Neikirk
- Department of Molecular Physiology and BiophysicsVanderbilt UniversityNashvilleTennesseeUSA
| | - Annet Kirabo
- Department of MedicineVanderbilt University Medical CenterNashvilleTennesseeUSA
- Vanderbilt Center for ImmunobiologyNashvilleTennesseeUSA
- Immunology and InflammationVanderbilt Institute for InfectionNashvilleTennesseeUSA
- Vanderbilt Institute for Global HealthNashvilleTennesseeUSA
| | - Monty Montano
- Department of MedicineHarvard Medical SchoolBostonMassachusettsUSA
| |
Collapse
|
4
|
Borrego-Ruiz A, Borrego JJ. Influence of human gut microbiome on the healthy and the neurodegenerative aging. Exp Gerontol 2024; 194:112497. [PMID: 38909763 DOI: 10.1016/j.exger.2024.112497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 05/16/2024] [Accepted: 06/17/2024] [Indexed: 06/25/2024]
Abstract
The gut microbiome plays a crucial role in host health throughout the lifespan by influencing brain function during aging. The microbial diversity of the human gut microbiome decreases during the aging process and, as a consequence, several mechanisms increase, such as oxidative stress, mitochondrial dysfunction, inflammatory response, and microbial gut dysbiosis. Moreover, evidence indicates that aging and neurodegeneration are closely related; consequently, the gut microbiome may serve as a novel marker of lifespan in the elderly. In this narrative study, we investigated how the changes in the composition of the gut microbiome that occur in aging influence to various neuropathological disorders, such as mild cognitive impairment (MCI), dementia, Alzheimer's disease (AD), and Parkinson's disease (PD); and which are the possible mechanisms that govern the relationship between the gut microbiome and cognitive impairment. In addition, several studies suggest that the gut microbiome may be a potential novel target to improve hallmarks of brain aging and to promote healthy cognition; therefore, current and future therapeutic interventions have been also reviewed.
Collapse
Affiliation(s)
- Alejandro Borrego-Ruiz
- Departamento de Psicología Social y de las Organizaciones, Universidad Nacional de Educación a Distancia (UNED), Madrid, Spain
| | - Juan J Borrego
- Departamento de Microbiología, Universidad de Málaga, Málaga, Spain; Instituto de Investigación Biomédica de Málaga y Plataforma en Nanomedicina-IBIMA, Plataforma BIONAND, Málaga, Spain.
| |
Collapse
|
5
|
Ferchiou S, Caza F, Sinha K, Sauvageau J, St-Pierre Y. Assessing marine ecosystem health using multi-omic analysis of blue mussel liquid biopsies: A case study within a national marine park. CHEMOSPHERE 2024; 362:142714. [PMID: 38950751 DOI: 10.1016/j.chemosphere.2024.142714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/03/2024]
Abstract
Marine ecosystems are under escalating threats from myriad environmental stressors, necessitating a deeper understanding of their impact on biodiversity and the health of sentinel organisms. In this study, we carried out a spatiotemporal multi-omic analysis of liquid biopsies collected from mussels (Mytilus spp.) in marine ecosystems of a national park. We delved into the epigenomic, transcriptomic, glycomic, proteomic, and microbiomic profiles to unravel the intricate interplay between ecosystem biodiversity and mussels' biological response to their environments. Our analysis revealed temporal fluctuations in the alpha diversity of the circulating microbiome associated with human activities. Analysis of the hemolymphatic circulating cell-free DNA (ccfDNA) provided information on the biodiversity and the presence of potential pathogens. Epigenomic analysis revealed widespread hypomethylation sites within the mitochondrial (mtDNA). Comparative transcriptomic and glycomic analyses highlighted differences in metabolic pathways and genes associated with immune and wound healing functions. This study demonstrates the potential of multi-omic analysis of liquid biopsy in sentinel to provide a holistic view of human activities' environmental impacts on marine coastal ecosystems. Overall, this approach has the potential to enhance the effectiveness and efficiency of various conservation efforts, leading to more informed decision-making and better outcomes for biodiversity and ecosystem conservation.
Collapse
Affiliation(s)
- Sophia Ferchiou
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, Canada, H7V 1B7
| | - France Caza
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, Canada, H7V 1B7
| | - Kumardip Sinha
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Janelle Sauvageau
- Human Health Therapeutics, National Research Council, 100 Sussex Dr., K1N 5A2, Ottawa, Ontario, Canada
| | - Yves St-Pierre
- INRS-Center Armand-Frappier Santé Technologie, 531 Boul. des Prairies, Laval, QC, Canada, H7V 1B7.
| |
Collapse
|
6
|
Kankanam Gamage SU, Hashimoto S, Miyamoto Y, Nakano T, Yamanaka M, Kitaji H, Takada Y, Matsumoto H, Koike A, Satoh M, Ichishi M, Watanabe M, Morimoto Y. Supplementation with autologous adipose stem cell-derived mitochondria can be a safe and promising strategy for improving oocyte quality. J Assist Reprod Genet 2024; 41:2065-2077. [PMID: 38777961 PMCID: PMC11339003 DOI: 10.1007/s10815-024-03137-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
PURPOSE In our previous study, we confirmed that the supplementation of vitrified-warmed murine oocytes with autologous adipose stem cell (ASC)-derived mitochondria during intracytoplasmic sperm injection enhances post-fertilization developmental competence in mice. To ensure the safety of this technology, we conducted a thorough study in mice to investigate the potential presence of specific malformations in offspring developed from this approach. METHODS A transgenerational comparative analysis was conducted on founder mice from embryos that developed after mitochondrial supplementation, and two subsequent generations. Reproductive performance, body growth rate, histopathological parameters, hematological parameters, daily activity patterns, and daily body temperature changes in male and female mice across these three generations were assessed in comparison to wild-type mice of the same age. RESULTS Both male and female animals in all three generations showed comparable reproductive performance to the control group. Additionally, body growth rate by the age of 8 weeks were found to be comparable to controls across all three generations. Notably, no significant histopathological abnormalities were detected in vital organs, including the brain, heart, liver, kidneys, lungs, ovaries, and testes, in any individuals from the studied cohorts. The blood parameters were consistent with the control data. The continuous monitoring of activity and body temperature changes (both day and night) over a 1-week period revealed a pattern closely resembling that observed in the control animals. CONCLUSION Injection of ASC-mitochondria into oocytes may be a promising technique to support developmental potential without causing adverse epigenetic events in the offspring in mice. However, before considering clinical application, additional safety screening using larger animals or non-human primates is essential.
Collapse
Affiliation(s)
| | - Shu Hashimoto
- Reproductive Science Institute, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | | | | | | | - Hideki Kitaji
- Reproductive Science Institute, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | - Yuki Takada
- Reproductive Science Institute, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Japan
| | | | - Akiko Koike
- HORAC Grand Front Osaka Clinic, Osaka, Japan
| | | | - Masako Ichishi
- Department of Oncologic Pathology, Graduate School of Medicine, Mie University, Mie, Japan
| | - Masatoshi Watanabe
- Department of Oncologic Pathology, Graduate School of Medicine, Mie University, Mie, Japan
| | | |
Collapse
|
7
|
Luo X, Liu P, Ye X, He J, Lai Y, Lv Y, Wu X, Liu Y, Zhang Q, Yang H, Wei W, Deng C, Kuang S, Wu S, Xue Y, Rao F. Curcumin improves atrial fibrillation susceptibility by regulating tsRNA expression in aging mouse atrium. PeerJ 2024; 12:e17495. [PMID: 39076782 PMCID: PMC11285363 DOI: 10.7717/peerj.17495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 05/09/2024] [Indexed: 07/31/2024] Open
Abstract
Age is an independent risk factor for atrial fibrillation (AF), and curcumin can delay aging related disease through reducing oxidative stress and inflammation. However, its target in aging-related AF remains unclear. Transfer RNA-derived small RNA (tsRNA) is a novel short non-coding RNA (sncRNA), and exerts a potential regulatory function in aging. This study was to explore the therapeutic targets of curcumin in atrium of aged mice by PANDORA-seq. Aged mice (18 month) were treated with curcumin (100 mg/kg). Rapid transjugular atrial pacing was performed to observe AF inducibility. SA-β-gal staining, reactive oxygen species (ROS) detection and qRT-PCR were used to assess the degree of aging and oxidative stress/inflammation levels. PANDORA-seq was performed to reveal the differentially expressed sncRNAs in the atrium of mice. The results showed that curcumin reduced the susceptibility AF of aged mice by improving aging-related atrial fibrosis. Compared to young mice (5 month) group, aged mice yielded 473 significantly altered tsRNA sequences, while 947 tsRNA sequences were significantly altered after treated with curcumin. Enrichment analysis revealed that the target genes were mainly related to DNA damage and protein modification. Compared with the 5 month group, the expression levels of mature-mt_tRNA-Val-TAC_CCA_end, mature-mt_tRNA-Glu-TTC_CCA_end, and mature-tRNA-Asp-GTC_CCA_end were up-regulated in the 18 month group, while the expression of mature-mt_tRNA-Thr-TGT_5_end was down-regulated. This trend was reversed in the 18 month + curcumin group. Increased cellular ROS levels, inflammation expression and senescence in aged mice atrium were improved by the down-regulation of mature-mt_tRNA-Val-TAC_CCA_end. In conclusion, our findings identified mature-mt_tRNA-Val-TAC_CCA_end participated in the mechanism of aging-related atrial fibrosis, providing new intervention target of aging-related AF.
Collapse
Affiliation(s)
- Xueshan Luo
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
- Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
- South China University of Technology, Guangzhou, Guangdong, China
| | - Panyue Liu
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
- South China University of Technology, Guangzhou, Guangdong, China
| | - Xingdong Ye
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Jintao He
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
- South China University of Technology, Guangzhou, Guangdong, China
| | - Yingyu Lai
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Yidong Lv
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Xiongbin Wu
- Jiangmen Central Hospital, Jiangmen, Guangdong, China
| | - Yang Liu
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Qianhuan Zhang
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Hui Yang
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Wei Wei
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Chunyu Deng
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
- South China University of Technology, Guangzhou, Guangdong, China
| | - Sujuan Kuang
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Shulin Wu
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
| | - Yumei Xue
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
- South China University of Technology, Guangzhou, Guangdong, China
| | - Fang Rao
- Guangdong Provincial Key Laboratory of Clinical Pharmacology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Southern Medical University, Guangzhou, Guangdong, China
- Guangdong Cardiovascular Institute, Guangzhou, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangdong, China
- South China University of Technology, Guangzhou, Guangdong, China
| |
Collapse
|
8
|
Zhang D, Deng W, Jiang T, Zhao Y, Bai D, Tian Y, Kong S, Zhang L, Wang H, Gao S, Lu Z. Maternal Ezh1/2 deficiency impairs the function of mitochondria in mouse oocytes and early embryos. J Cell Physiol 2024; 239:e31244. [PMID: 38529784 DOI: 10.1002/jcp.31244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/23/2024] [Accepted: 02/27/2024] [Indexed: 03/27/2024]
Abstract
Maternal histone methyltransferase is critical for epigenetic regulation and development of mammalian embryos by regulating histone and DNA modifications. Here, we reported a novel mechanism by revealing the critical effects of maternal Ezh1/2 deletion on mitochondria in MII oocytes and early embryos in mice. We found that Ezh1/2 knockout in mouse MII oocytes impaired the structure of mitochondria and decreased its number, but membrane potential and respiratory function of mitochondrion were increased. The similar effects of Ezh1/2 deletion have been observed in 2-cell and morula embryos, indicating that the effects of maternal Ezh1/2 deficiency on mitochondrion extend to early embryos. However, the loss of maternal Ezh1/2 resulted in a severe defect of morula: the number, membrane potential, respiratory function, and ATP production of mitochondrion dropped significantly. Content of reactive oxygen species was raised in both MII oocytes and early embryos, suggesting maternal Ezh1/2 knockout induced oxidative stress. In addition, maternal Ezh1/2 ablation interfered the autophagy in morula and blastocyst embryos. Finally, maternal Ezh1/2 deletion led to cell apoptosis in blastocyst embryos in mice. By analyzing the gene expression profile, we revealed that maternal Ezh1/2 knockout affected the expression of mitochondrial related genes in MII oocytes and early embryos. The chromatin immunoprecipitation-polymerase chain reaction assay demonstrated that Ezh1/2 directly regulated the expression of genes Fxyd6, Adpgk, Aurkb, Zfp521, Ehd3, Sgms2, Pygl, Slc1a1, and Chst12 by H3K27me3 modification. In conclusion, our study revealed the critical effect of maternal Ezh1/2 on the structure and function of mitochondria in oocytes and early embryos, and suggested a novel mechanism underlying maternal epigenetic regulation on early embryonic development through the modulation of mitochondrial status.
Collapse
Affiliation(s)
- Dan Zhang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, China
| | - Wenbo Deng
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Ting Jiang
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, China
| | - Yinan Zhao
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, China
| | - Dandan Bai
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Yingpu Tian
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, China
| | - Shuangbo Kong
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Leilei Zhang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Haibin Wang
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Shaorong Gao
- Shanghai Key Laboratory of Signaling and Disease Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Zhongxian Lu
- School of Pharmaceutical Sciences, Fujian Provincial Key Laboratory of Innovative Drug Target Research, Xiamen University, Xiamen, Fujian, China
- Fujian Provincial Key Laboratory of Reproductive Health Research, Department of Obstetrics and Gynecology, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| |
Collapse
|
9
|
Li W, Li Y, Zhao J, Liao J, Wen W, Chen Y, Cui H. Release of damaged mitochondrial DNA: A novel factor in stimulating inflammatory response. Pathol Res Pract 2024; 258:155330. [PMID: 38733868 DOI: 10.1016/j.prp.2024.155330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/03/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024]
Abstract
Mitochondrial DNA (mtDNA) is a circular double-stranded genome that exists independently of the nucleus. In recent years, research on mtDNA has significantly increased, leading to a gradual increase in understanding of its physiological and pathological characteristics. Reactive oxygen species (ROS) and other factors can damage mtDNA. This damaged mtDNA can escape from the mitochondria to the cytoplasm or extracellular space, subsequently activating immune signaling pathways, such as NLR family pyrin domain protein 3 (NLRP3), and triggering inflammatory responses. Numerous studies have demonstrated the involvement of mtDNA damage and leakage in the pathological mechanisms underlying various diseases including infectious diseases, metabolic inflammation, and immune disorders. Consequently, comprehensive investigation of mtDNA can elucidate the pathological mechanisms underlying numerous diseases. The prevention of mtDNA damage and leakage has emerged as a novel approach to disease treatment, and mtDNA has emerged as a promising target for drug development. This article provides a comprehensive review of the mechanisms underlying mtDNA-induced inflammation, its association with various diseases, and the methods used for its detection.
Collapse
Affiliation(s)
- Wenting Li
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Yunnan 650500, China
| | - Yuting Li
- First Teaching Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
| | - Jie Zhao
- Department of TCM Endocrinology, Yunnan Provincial Hospital of Traditional Chinese Medicine, Yunnan 650021, China
| | - Jiabao Liao
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Yunnan 650500, China
| | - Weibo Wen
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Yunnan 650500, China.
| | - Yao Chen
- Department of TCM Encephalopathy, Yunnan Provincial Hospital of Traditional Chinese Medicine, Yunnan 650021, China.
| | - Huantian Cui
- The First School of Clinical Medicine, Yunnan University of Chinese Medicine, Yunnan 650500, China.
| |
Collapse
|
10
|
Villa C, Combi R. Epigenetics in Alzheimer's Disease: A Critical Overview. Int J Mol Sci 2024; 25:5970. [PMID: 38892155 PMCID: PMC11173284 DOI: 10.3390/ijms25115970] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Epigenetic modifications have been implicated in a number of complex diseases as well as being a hallmark of organismal aging. Several reports have indicated an involvement of these changes in Alzheimer's disease (AD) risk and progression, most likely contributing to the dysregulation of AD-related gene expression measured by DNA methylation studies. Given that DNA methylation is tissue-specific and that AD is a brain disorder, the limitation of these studies is the ability to identify clinically useful biomarkers in a proxy tissue, reflective of the tissue of interest, that would be less invasive, more cost-effective, and easily obtainable. The age-related DNA methylation changes have also been used to develop different generations of epigenetic clocks devoted to measuring the aging in different tissues that sometimes suggests an age acceleration in AD patients. This review critically discusses epigenetic changes and aging measures as potential biomarkers for AD detection, prognosis, and progression. Given that epigenetic alterations are chemically reversible, treatments aiming at reversing these modifications will be also discussed as promising therapeutic strategies for AD.
Collapse
Affiliation(s)
| | - Romina Combi
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy;
| |
Collapse
|
11
|
Nikolic A, Fahlbusch P, Riffelmann NK, Wahlers N, Jacob S, Hartwig S, Kettel U, Schiller M, Dille M, Al-Hasani H, Kotzka J, Knebel B. Chronic stress alters hepatic metabolism and thermodynamic respiratory efficiency affecting epigenetics in C57BL/6 mice. iScience 2024; 27:109276. [PMID: 38450153 PMCID: PMC10915629 DOI: 10.1016/j.isci.2024.109276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 03/08/2024] Open
Abstract
Chronic stress episodes increase metabolic disease risk even after recovery. We propose that persistent stress detrimentally impacts hepatic metabolic reprogramming, particularly mitochondrial function. In male C57BL/6 mice chronic variable stress (Cvs) reduced energy expenditure (EE) and body mass despite increased energy intake versus controls. This coincided with decreased glucose metabolism and increased lipid β-oxidation, correlating with EE. After Cvs, mitochondrial function revealed increased thermodynamic efficiency (ƞ-opt) of complex CI, positively correlating with blood glucose and NEFA and inversely with EE. After Cvs recovery, the metabolic flexibility of hepatocytes was lost. Reduced CI-driving NAD+/NADH ratio, and diminished methylation-related one-carbon cycle components hinted at epigenetic regulation. Although initial DNA methylation differences were minimal after Cvs, they diverged during the recovery phase. Here, the altered enrichment of mitochondrial DNA methylation and linked transcriptional networks were observed. In conclusion, Cvs rapidly initiates the reprogramming of hepatic energy metabolism, supported by lasting epigenetic modifications.
Collapse
Affiliation(s)
- Aleksandra Nikolic
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, 40225 Duesseldorf, Germany
| | - Pia Fahlbusch
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, 40225 Duesseldorf, Germany
| | - Nele-Kathrien Riffelmann
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
| | - Natalie Wahlers
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
| | - Sylvia Jacob
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
| | - Sonja Hartwig
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, 40225 Duesseldorf, Germany
| | - Ulrike Kettel
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
| | - Martina Schiller
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
| | - Matthias Dille
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
| | - Hadi Al-Hasani
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, 40225 Duesseldorf, Germany
- Medical Faculty Heinrich-Heine-University Düsseldorf, 40225 Düsseldorf, Germany
| | - Jörg Kotzka
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, 40225 Duesseldorf, Germany
| | - Birgit Knebel
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Duesseldorf, Leibniz Center for Diabetes Research, 40225 Duesseldorf, Germany
- German Center for Diabetes Research (DZD), Partner Duesseldorf, 40225 Duesseldorf, Germany
| |
Collapse
|
12
|
Park JH, Sahbaz BD, Pekhale K, Chu X, Okur MN, Grati M, Isgrig K, Chien W, Chrysostomou E, Sullivan L, Croteau DL, Manor U, Bohr VA. Early-Onset Hearing Loss in Mouse Models of Alzheimer's Disease and Increased DNA Damage in the Cochlea. AGING BIOLOGY 2024; 1:20240025. [PMID: 38500536 PMCID: PMC10948084 DOI: 10.59368/agingbio.20240025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
There is considerable interest in whether sensory deficiency is associated with the development of Alzheimer's disease (AD). Notably, the relationship between hearing impairment and AD is of high relevance but still poorly understood. In this study, we found early-onset hearing loss in two AD mouse models, 3xTgAD and 3xTgAD/Polβ+/-. The 3xTgAD/Polβ+/- mouse is DNA repair deficient and has more humanized AD features than the 3xTgAD. Both AD mouse models showed increased auditory brainstem response (ABR) thresholds between 16 and 32 kHz at 4 weeks of age, much earlier than any AD cognitive and behavioral changes. The ABR thresholds were significantly higher in 3xTgAD/Polβ+/- mice than in 3xTgAD mice at 16 kHz, and distortion product otoacoustic emission signals were reduced, indicating that DNA damage may be a factor underlying early hearing impairment in AD. Poly ADP-ribosylation and protein expression levels of DNA damage markers increased significantly in the cochlea of the AD mice but not in the adjacent auditory cortex. Phosphoglycerate mutase 2 levels and the number of synaptic ribbons in the presynaptic zones of inner hair cells were decreased in the cochlea of the AD mice. Furthermore, the activity of sirtuin 3 was downregulated in the cochlea of these mice, indicative of impaired mitochondrial function. Taken together, these findings provide new insights into potential mechanisms for hearing dysfunction in AD and suggest that DNA damage in the cochlea might contribute to the development of early hearing loss in AD.
Collapse
Affiliation(s)
- Jae-Hyeon Park
- DNA repair Section, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Burcin Duan Sahbaz
- DNA repair Section, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Komal Pekhale
- DNA repair Section, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Xixia Chu
- DNA repair Section, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Mustafa N. Okur
- DNA repair Section, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Mhamed Grati
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Kevin Isgrig
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
| | - Wade Chien
- National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Bethesda, MD, USA
- Department of Otolaryngology-Head & Neck Surgery, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Elena Chrysostomou
- Waitt Advanced Biophotonics Center, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Lauren Sullivan
- Department of Cell & Developmental Biology School of Biological Sciences University of California, San Diego, La Jolla, CA, USA
| | - Deborah L. Croteau
- DNA repair Section, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
- Computational Biology & Genomics Core, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Uri Manor
- Department of Cell & Developmental Biology School of Biological Sciences University of California, San Diego, La Jolla, CA, USA
| | - Vilhelm A. Bohr
- DNA repair Section, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
- Danish Center for Healthy Aging, University of Copenhagen, Copenhagen N, Denmark
| |
Collapse
|
13
|
Braden AA, Xiao J, Hori R, Brown C, Khan MM. An Overview of UBTF Neuroregression Syndrome. Brain Sci 2024; 14:179. [PMID: 38391753 PMCID: PMC10886456 DOI: 10.3390/brainsci14020179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/24/2024] Open
Abstract
Recently, a recurrent de novo dominant mutation in UBTF (c.628G>A, p.Glu210Lys; UBTF E210K) was identified as the cause of a neurological disorder which has been named UBTF Neuroregression Syndrome (UNS), or Childhood-Onset Neurodegeneration with Brain Atrophy (CONDBA). To date, only 17 cases have been reported worldwide. The molecular etiology is a pathogenic variant, E210K, within the HMG-box 2 of Upstream Binding Transcription Factor (UBTF). UBTF, a nucleolar protein, plays an important role in ribosomal RNA (rRNA) synthesis, nucleolar integrity, and cell survival. This variant causes unstable preinitiation complexes to form, resulting in altered rDNA chromatin structures, rRNA dysregulation, DNA damage, and ultimately, neurodegeneration. Defining clinical characteristics of the disorder include but are not limited to developmental regression beginning at approximately three years of age, progressive motor dysfunction, declining cognition, ambulatory loss, and behavioral problems. Histological and neuroimaging abnormalities include cortical atrophy, white matter deficits, and enlarged ventricles. Herein, we present a detailed overview of all published cases as well as the functional roles of UBTF to better understand the pathophysiology. Bringing undiagnosed cases to the attention of clinicians and researchers by making them aware of the clinical features will improve research and support the development of therapeutic interventions.
Collapse
Affiliation(s)
- Anneliesse A Braden
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38104, USA
- Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jianfeng Xiao
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38104, USA
| | - Roderick Hori
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Chester Brown
- Department of Pediatrics, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Mohammad Moshahid Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38104, USA
- Neuroscience Institute, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Division of Regenerative and Rehabilitation Sciences, Department of Physical Therapy, Center for Muscle, Metabolism and Neuropathology, College of Health Professions, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| |
Collapse
|
14
|
Nguyen J, Win PW, Nagano TS, Shin EH, Newcomb C, Arking DE, Castellani CA. Mitochondrial DNA copy number reduction via in vitro TFAM knockout remodels the nuclear epigenome and transcriptome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.29.577835. [PMID: 38352513 PMCID: PMC10862824 DOI: 10.1101/2024.01.29.577835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/22/2024]
Abstract
Mitochondrial DNA copy number (mtDNA-CN) is associated with several age-related chronic diseases and is a predictor of all-cause mortality. Here, we examine site-specific differential nuclear DNA (nDNA) methylation and differential gene expression resulting from in vitro reduction of mtDNA-CN to uncover shared genes and biological pathways mediating the effect of mtDNA-CN on disease. Epigenome and transcriptome profiles were generated for three independent human embryonic kidney (HEK293T) cell lines harbouring a mitochondrial transcription factor A (TFAM) heterozygous knockout generated via CRISPR-Cas9, and matched control lines. We identified 4,242 differentially methylated sites, 228 differentially methylated regions, and 179 differentially expressed genes associated with mtDNA-CN. Integrated analysis uncovered 381 Gene-CpG pairs. GABAA receptor genes and related pathways, the neuroactive ligand receptor interaction pathway, ABCD1/2 gene activity, and cell signalling processes were overrepresented, providing insight into the underlying biological mechanisms facilitating these associations. We also report evidence implicating chromatin state regulatory mechanisms as modulators of mtDNA-CN effect on gene expression. We demonstrate that mitochondrial DNA variation signals to the nuclear DNA epigenome and transcriptome and may lead to nuclear remodelling relevant to development, aging, and complex disease.
Collapse
Affiliation(s)
- Julia Nguyen
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Phyo W. Win
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Tyler Shin Nagano
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Elly H. Shin
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
| | - Charles Newcomb
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Dan E. Arking
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Christina A. Castellani
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- Department of Epidemiology and Biostatistics, Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Children’s Health Research Institute, Lawson Research Institute, London, Ontario, Canada
| |
Collapse
|
15
|
Ceylan D, Arat-Çelik HE, Aksahin IC. Integrating mitoepigenetics into research in mood disorders: a state-of-the-art review. Front Physiol 2024; 15:1338544. [PMID: 38410811 PMCID: PMC10895490 DOI: 10.3389/fphys.2024.1338544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/24/2024] [Indexed: 02/28/2024] Open
Abstract
Mood disorders, including major depressive disorder and bipolar disorder, are highly prevalent and stand among the leading causes of disability. Despite the largely elusive nature of the molecular mechanisms underpinning these disorders, two pivotal contributors-mitochondrial dysfunctions and epigenetic alterations-have emerged as significant players in their pathogenesis. This state-of-the-art review aims to present existing data on epigenetic alterations in the mitochondrial genome in mood disorders, laying the groundwork for future research into their pathogenesis. Associations between abnormalities in mitochondrial function and mood disorders have been observed, with evidence pointing to notable changes in mitochondrial DNA (mtDNA). These changes encompass variations in copy number and oxidative damage. However, information on additional epigenetic alterations in the mitochondrial genome remains limited. Recent studies have delved into alterations in mtDNA and regulations in the mitochondrial genome, giving rise to the burgeoning field of mitochondrial epigenetics. Mitochondrial epigenetics encompasses three main categories of modifications: mtDNA methylation/hydroxymethylation, modifications of mitochondrial nucleoids, and mitochondrial RNA alterations. The epigenetic modulation of mitochondrial nucleoids, lacking histones, may impact mtDNA function. Additionally, mitochondrial RNAs, including non-coding RNAs, present a complex landscape influencing interactions between the mitochondria and the nucleus. The exploration of mitochondrial epigenetics offers valuable perspectives on how these alterations impact neurodegenerative diseases, presenting an intriguing avenue for research on mood disorders. Investigations into post-translational modifications and the role of mitochondrial non-coding RNAs hold promise to unravel the dynamics of mitoepigenetics in mood disorders, providing crucial insights for future therapeutic interventions.
Collapse
Affiliation(s)
- Deniz Ceylan
- Department of Psychiatry, School of Medicine, Koç University, Istanbul, Türkiye
- Koç University Research Center for Translational Medicine (KUTTAM), Affective Laboratory, Istanbul, Türkiye
| | | | - Izel Cemre Aksahin
- Koç University Research Center for Translational Medicine (KUTTAM), Affective Laboratory, Istanbul, Türkiye
- Graduate School of Health Sciences, Koç University, Istanbul, Türkiye
| |
Collapse
|
16
|
Gao Y, Guo L, Wang F, Wang Y, Li P, Zhang D. Development of mitochondrial gene-editing strategies and their potential applications in mitochondrial hereditary diseases: a review. Cytotherapy 2024; 26:11-24. [PMID: 37930294 DOI: 10.1016/j.jcyt.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023]
Abstract
Mitochondrial DNA (mtDNA) is a critical genome contained within the mitochondria of eukaryotic cells, with many copies present in each mitochondrion. Mutations in mtDNA often are inherited and can lead to severe health problems, including various inherited diseases and premature aging. The lack of efficient repair mechanisms and the susceptibility of mtDNA to damage exacerbate the threat to human health. Heteroplasmy, the presence of different mtDNA genotypes within a single cell, increases the complexity of these diseases and requires an effective editing method for correction. Recently, gene-editing techniques, including programmable nucleases such as restriction endonuclease, zinc finger nuclease, transcription activator-like effector nuclease, clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated 9 and base editors, have provided new tools for editing mtDNA in mammalian cells. Base editors are particularly promising because of their high efficiency and precision in correcting mtDNA mutations. In this review, we discuss the application of these techniques in mitochondrial gene editing and their limitations. We also explore the potential of base editors for mtDNA modification and discuss the opportunities and challenges associated with their application in mitochondrial gene editing. In conclusion, this review highlights the advancements, limitations and opportunities in current mitochondrial gene-editing technologies and approaches. Our insights aim to stimulate the development of new editing strategies that can ultimately alleviate the adverse effects of mitochondrial hereditary diseases.
Collapse
Affiliation(s)
- Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Linlin Guo
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
| |
Collapse
|
17
|
Mizuno G, Yamada H, Tsuboi Y, Munetsuna E, Yamazaki M, Ando Y, Kageyama I, Nouchi Y, Teshigawara A, Hattori Y, Fujii R, Ishikawa H, Hashimoto S, Ohashi K, Hamajima N, Suzuki K. Low mitochondrial DNA copy number in peripheral blood mononuclear cells is associated with future mortality risk: a long-term follow-up study from Japan. J Nutr Health Aging 2024; 28:100013. [PMID: 38267162 DOI: 10.1016/j.jnha.2023.100013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 11/16/2023] [Indexed: 01/26/2024]
Abstract
OBJECTIVES The mitochondrial DNA (mtDNA) is unique and circular with multiple copies of the genome. The lower mtDNA copy number (mtDNA-CN) in leukocytes is associated with the risk of all-cause mortality. However, its long-term association is unknown. Thus, the study examined the association between mtDNA-CN and the risk of all-cause mortality in a long-term follow-up study in the Japanese population. DESIGN This longitudinal study included the study cohort from an annual, population-based health checkup in the town of Yakumo, Hokkaido, Japan. SETTING AND PARTICIPANTS 814 participants (baseline age range: 38-80 years, mean: 56.3 years) were included in this study in 1990. They were followed-up regarding mortality for about 30 years (median: 28.1 years) till 2019. MEASURES The genomic DNA was extracted from peripheral blood mononuclear cells and the mtDNA-CN was measured using real-time polymerase chain reaction. The level of the mtDNA-CN was divided into tertiles (low, middle, and high). The participants were categorized based on their age into middle-aged (<60 years old) or old-aged (≥60 years old). Survival analysis was performed for tertile of mtDNA-CN and compared using the log-rank test. Univariate and multivariable Cox proportional hazard regression analyses were performed to assess the association between mtDNA-CN and all-cause mortality. The model adjusted with age, sex, body mass index, systolic blood pressure, smoking habit, alcohol consumption, exercise habit, and education level. RESULTS The low levels of mtDNA-CN resulted in a significant decrease in cumulative survival rate (P < 0.05). The risk of mortality was significantly higher in the middle-aged cohort when mtDNA-CN levels were low (hazard ratios [95% confidence intervals]: 1.98 [1.10-3.56]). CONCLUSION This study demonstrated that leukocyte mtDNA-CN is associated with future mortality risk. Our study findings may lead to further research on the early prediction of mortality and its underlying mechanisms.
Collapse
Affiliation(s)
- Genki Mizuno
- Department of Medical Technology, Tokyo University of Technology School of Health Sciences, 5-23-22 Nishi-Kamata, Ota, Tokyo, 144-8535, Japan; Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Hiroya Yamada
- Department of Hygiene, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan.
| | - Yoshiki Tsuboi
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Eiji Munetsuna
- Department of Animal Science and Biotechnology, Azabu University School of Veterinary Medicine, 1-17-71 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5201, Japan
| | - Mirai Yamazaki
- Department of Hygiene, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan; Department of Medical Technology, Kagawa Prefectural University of Health Sciences, 281-1 Hara, Mure-cho, Takamatsu, Kagawa 761-0123, Japan
| | - Yoshitaka Ando
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Itsuki Kageyama
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Yuki Nouchi
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Atsushi Teshigawara
- Department of Joint Research Laboratory of Clinical Medicine, Fujita Health University Hospital, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Yuji Hattori
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Ryosuke Fujii
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Hiroaki Ishikawa
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Shuji Hashimoto
- Department of Hygiene, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Koji Ohashi
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan
| | - Nobuyuki Hamajima
- Department of Healthcare Administration, Nagoya University Graduate School of Medicine, Nagoya, Aichi 466-8550, Japan
| | - Koji Suzuki
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Aichi 470-1192, Japan.
| |
Collapse
|
18
|
Alves CAPF, Whitehead MT. Advancing the neuroimaging diagnosis and understanding of mitochondrial disorders. Neurotherapeutics 2024; 21:e00324. [PMID: 38306952 PMCID: PMC10903090 DOI: 10.1016/j.neurot.2024.e00324] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/16/2024] [Accepted: 01/16/2024] [Indexed: 02/04/2024] Open
Abstract
Mitochondrial diseases, a diverse and intricate group of disorders, result from both nuclear DNA and mitochondrial DNA malfunctions, leading to a decrease in cellular energy (ATP) production. The increasing understanding of molecular, biochemical, and genetic irregularities associated with mitochondrial dysfunction has led to a wider recognition of varying mitochondrial disease phenotypes. This broadening landscape has led to a diverse array of neuroimaging findings, posing a challenge to radiologists in identifying the extensive range of possible patterns. This review meticulously describes the central imaging features of mitochondrial diseases in children, as revealed by neuroimaging. It spans from traditional imaging findings to more recent and intricate diagnoses, offering insights and highlighting advancements in neuroimaging technology that can potentially guide a more efficient and accurate diagnostic approach.
Collapse
Affiliation(s)
- César Augusto P F Alves
- Division of Neuroradiology, Department of Radiology, Boston Children's Hospital - BCH Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, United States.
| | - Matthew T Whitehead
- Division of Neuroradiology, Department of Radiology, The Children's Hospital of Philadelphia, PA, United States; Perelman School of Medicine, University of Pennsylvania Perelman School of Medicine of Philadelphia, United States.
| |
Collapse
|
19
|
La Colla A, Cámara CA, Campisano S, Chisari AN. Mitochondrial dysfunction and epigenetics underlying the link between early-life nutrition and non-alcoholic fatty liver disease. Nutr Res Rev 2023; 36:281-294. [PMID: 35067233 DOI: 10.1017/s0954422422000038] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Early-life malnutrition plays a critical role in foetal development and predisposes to metabolic diseases later in life, according to the concept of 'developmental programming'. Different types of early nutritional imbalance, including undernutrition, overnutrition and micronutrient deficiency, have been related to long-term metabolic disorders. Accumulating evidence has demonstrated that disturbances in nutrition during the period of preconception, pregnancy and primary infancy can affect mitochondrial function and epigenetic mechanisms. Moreover, even though multiple mechanisms underlying non-alcoholic fatty liver disease (NAFLD) have been described, in the past years, special attention has been given to mitochondrial dysfunction and epigenetic alterations. Mitochondria play a key role in cellular metabolic functions. Dysfunctional mitochondria contribute to oxidative stress, insulin resistance and inflammation. Epigenetic mechanisms have been related to alterations in genes involved in lipid metabolism, fibrogenesis, inflammation and tumorigenesis. In accordance, studies have reported that mitochondrial dysfunction and epigenetics linked to early-life nutrition can be important contributing factors in the pathogenesis of NAFLD. In this review, we summarise the current understanding of the interplay between mitochondrial dysfunction, epigenetics and nutrition during early life, which is relevant to developmental programming of NAFLD.
Collapse
Affiliation(s)
- Anabela La Colla
- Departamento de Química y Bioquímica, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Carolina Anahí Cámara
- Departamento de Química y Bioquímica, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Sabrina Campisano
- Departamento de Química y Bioquímica, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| | - Andrea Nancy Chisari
- Departamento de Química y Bioquímica, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Mar del Plata, 7600 Mar del Plata, Argentina
| |
Collapse
|
20
|
Cossin-Sevrin N, Stier A, Hukkanen M, Zahn S, Viblanc VA, Anttila K, Ruuskanen S. Early-life environmental effects on mitochondrial aerobic metabolism: a brood size manipulation in wild great tits. J Exp Biol 2023; 226:jeb245932. [PMID: 37815441 DOI: 10.1242/jeb.245932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023]
Abstract
In avian species, the number of chicks in the nest and subsequent sibling competition for food are major components of the offspring's early-life environment. A large brood size is known to affect chick growth, leading in some cases to long-lasting effects for the offspring, such as a decrease in size at fledgling and in survival after fledging. An important pathway underlying different growth patterns could be the variation in offspring mitochondrial metabolism through its central role in converting energy. Here, we performed a brood size manipulation in great tits (Parus major) to unravel its impact on offspring mitochondrial metabolism and reactive oxygen species (ROS) production in red blood cells. We investigated the effects of brood size on chick growth and survival, and tested for long-lasting effects on juvenile mitochondrial metabolism and phenotype. As expected, chicks raised in reduced broods had a higher body mass compared with enlarged and control groups. However, mitochondrial metabolism and ROS production were not significantly affected by the treatment at either chick or juvenile stages. Interestingly, chicks raised in very small broods were smaller in size and had higher mitochondrial metabolic rates. The nest of rearing had a significant effect on nestling mitochondrial metabolism. The contribution of the rearing environment in determining offspring mitochondrial metabolism emphasizes the plasticity of mitochondrial metabolism in relation to the nest environment. This study opens new avenues regarding the effect of postnatal environmental conditions in shaping offspring early-life mitochondrial metabolism.
Collapse
Affiliation(s)
- Nina Cossin-Sevrin
- Department of Biology, University of Turku, FI-20014 Turku, Finland
- Université de Strasbourg, Centre National de la Recherche Scientifique, Institut Pluridisciplinaire Hubert Curien, UMR 7178, 67087 Strasbourg, France
| | - Antoine Stier
- Department of Biology, University of Turku, FI-20014 Turku, Finland
- Université de Strasbourg, Centre National de la Recherche Scientifique, Institut Pluridisciplinaire Hubert Curien, UMR 7178, 67087 Strasbourg, France
- Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, F-69622 Villeurbanne, France
| | - Mikaela Hukkanen
- Institute for Molecular Medicine Finland, University of Helsinki, FI-00014 Helsinki, Finland
| | - Sandrine Zahn
- Université de Strasbourg, Centre National de la Recherche Scientifique, Institut Pluridisciplinaire Hubert Curien, UMR 7178, 67087 Strasbourg, France
| | - Vincent A Viblanc
- Université de Strasbourg, Centre National de la Recherche Scientifique, Institut Pluridisciplinaire Hubert Curien, UMR 7178, 67087 Strasbourg, France
| | - Katja Anttila
- Department of Biology, University of Turku, FI-20014 Turku, Finland
| | - Suvi Ruuskanen
- Department of Biology, University of Turku, FI-20014 Turku, Finland
- Department of Biological and Environmental Sciences, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| |
Collapse
|
21
|
Kim JH, Mun SJ, Kim JH, Son MJ, Kim SY. Integrative analysis of single-cell RNA-seq and ATAC-seq reveals heterogeneity of induced pluripotent stem cell-derived hepatic organoids. iScience 2023; 26:107675. [PMID: 37680467 PMCID: PMC10481365 DOI: 10.1016/j.isci.2023.107675] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/30/2023] [Accepted: 08/14/2023] [Indexed: 09/09/2023] Open
Abstract
To gain deeper insights into transcriptomes and epigenomes of organoids, liver organoids from two states (expandable and more differentiated) were subjected to single-cell RNA-seq (scRNA-seq) and single-cell ATAC-seq (scATAC-seq) analyses. Mitochondrial gene expression was higher in differentiated than in non-differentiated hepatocytes, with ATAC-seq peaks increasing near the mitochondrial control region. Differentiation of liver organoids resulted in the expression of transcription factors that act as enhancers and repressors. In addition, epigenetic mechanisms regulating the expression of alpha-fetoprotein (AFP) and albumin (ALB) differed in liver organoids and adult liver. Knockdown of PDX1, an essential transcription factor for pancreas development, led to the hepatic maturation of liver organoids through regulation of AFP and ALB expression. This integrative analysis of the transcriptomes and epigenomes of liver organoids at the single-cell level may contribute to a better understanding of the regulatory networks during liver development and the further development of mature in vitro human liver models.
Collapse
Affiliation(s)
| | - Seon Ju Mun
- Stem Cell Convergence Research Center, Daejeon, Korea
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, Korea
| | - Jeong-Hwan Kim
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
| | - Myung Jin Son
- Stem Cell Convergence Research Center, Daejeon, Korea
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, Korea
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Seon-Young Kim
- Korean Bioinformation Center, Daejeon, Korea
- Personalized Genomic Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Korea
- Department of Functional Genomics, University of Science and Technology (UST), Daejeon, Korea
| |
Collapse
|
22
|
Ma Y, Du J, Chen M, Gao N, Wang S, Mi Z, Wei X, Zhao J. Mitochondrial DNA methylation is a predictor of immunotherapy response and prognosis in breast cancer: scRNA-seq and bulk-seq data insights. Front Immunol 2023; 14:1219652. [PMID: 37457713 PMCID: PMC10339346 DOI: 10.3389/fimmu.2023.1219652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023] Open
Abstract
Background Alterations in Mitochondrial DNA methylation (MTDM) exist in many tumors, but their role in breast cancer (BC) development remains unclear. Methods We analyzed BC patient data by combining scRNA-seq and bulk sequencing. Weighted co-expression network analysis (WGCNA) of TCGA data identified mitochondrial DNA methylation (MTDM)-associated genes in BC. COX regression and LASSO regression were used to build prognostic models. The biological function of MTDM was assessed using various methods, such as signaling pathway enrichment analysis, copynumber karyotyping analysis, and quantitative analysis of the cell proliferation rate. We also evaluated MTDM-mediated alterations in the immune microenvironment using immune microenvironment, microsatellite instability, mutation, unsupervised clustering, malignant cell subtype differentiation, immune cell subtype differentiation, and cell-communication signature analyses. Finally, we performed cellular experiments to validate the role of the MTDM-associated prognostic gene NCAPD3 in BC. Results In this study, MTDM-associated prognostic models divided BC patients into high/low MTDM groups in TCGA/GEO datasets. The difference in survival time between the two groups was statistically significant (P<0.001). We found that high MTDM status was positively correlated with tumor cell proliferation. We analyzed the immune microenvironment and found that low-MTDM group had higher immune checkpoint gene expression/immune cell infiltration, which could lead to potential benefits from immunotherapy. In contrast, the high MTDM group had higher proliferation rates and levels of CD8+T cell exhaustion, which may be related to the secretion of GDF15 by malignant breast epithelial cells with a high MTDM status. Cellular experiments validated the role of the MTDM-associated prognostic gene NCAPD3 (the gene most positively correlated with epithelial malignant cell proliferation in the model) in BC. Knockdown of NCAPD3 significantly reduced the activity and proliferation of MDA-MB-231 and BCAP-37 cells, and significantly reduced their migration ability of BCAP-37 cell line. Conclusion This study presented a holistic evaluation of the multifaceted roles of MTDM in BC. The analysis of MTDM levels not only enables the prediction of response to immunotherapy but also serves as an accurate prognostic indicator for patients with BC. These insightful discoveries provide novel perspectives on tumor immunity and have the potentially to revolutionize the diagnosis and treatment of BC.
Collapse
|
23
|
Kapinova A, Mazurakova A, Halasova E, Dankova Z, Büsselberg D, Costigliola V, Golubnitschaja O, Kubatka P. Underexplored reciprocity between genome-wide methylation status and long non-coding RNA expression reflected in breast cancer research: potential impacts for the disease management in the framework of 3P medicine. EPMA J 2023; 14:249-273. [PMID: 37275549 PMCID: PMC10236066 DOI: 10.1007/s13167-023-00323-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
Breast cancer (BC) is the most common female malignancy reaching a pandemic scale worldwide. A comprehensive interplay between genetic alterations and shifted epigenetic regions synergistically leads to disease development and progression into metastatic BC. DNA and histones methylations, as the most studied epigenetic modifications, represent frequent and early events in the process of carcinogenesis. To this end, long non-coding RNAs (lncRNAs) are recognized as potent epigenetic modulators in pathomechanisms of BC by contributing to the regulation of DNA, RNA, and histones' methylation. In turn, the methylation status of DNA, RNA, and histones can affect the level of lncRNAs expression demonstrating the reciprocity of mechanisms involved. Furthermore, lncRNAs might undergo methylation in response to actual medical conditions such as tumor development and treated malignancies. The reciprocity between genome-wide methylation status and long non-coding RNA expression levels in BC remains largely unexplored. Since the bio/medical research in the area is, per evidence, strongly fragmented, the relevance of this reciprocity for BC development and progression has not yet been systematically analyzed. Contextually, the article aims at:consolidating the accumulated knowledge on both-the genome-wide methylation status and corresponding lncRNA expression patterns in BC andhighlighting the potential benefits of this consolidated multi-professional approach for advanced BC management. Based on a big data analysis and machine learning for individualized data interpretation, the proposed approach demonstrates a great potential to promote predictive diagnostics and targeted prevention in the cost-effective primary healthcare (sub-optimal health conditions and protection against the health-to-disease transition) as well as advanced treatment algorithms tailored to the individualized patient profiles in secondary BC care (effective protection against metastatic disease). Clinically relevant examples are provided, including mitochondrial health control and epigenetic regulatory mechanisms involved.
Collapse
Affiliation(s)
- Andrea Kapinova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Alena Mazurakova
- Department of Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Erika Halasova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Dietrich Büsselberg
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, 24144 Doha, Qatar
| | | | - Olga Golubnitschaja
- Predictive, Preventive, and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| |
Collapse
|
24
|
Fan X, Zhang D, Hou T, Zhang Q, Wang Z. Insight into the health risk implicated in mitochondrial toxicity of dibutyl phthalate exposure on zebrafish (Danio rerio) cells. CHEMOSPHERE 2023; 326:138510. [PMID: 36966926 DOI: 10.1016/j.chemosphere.2023.138510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/06/2023] [Accepted: 03/24/2023] [Indexed: 06/18/2023]
Abstract
Dibutyl phthalate (DBP) is commonly applied plasticizer in plastic products such as face masks, easily leaches or migrates into environment and its widespread contamination posed profound health risks. Further concerns rise regarding to the toxicity of DBP at subcellular level, while little is known about the ranging effects on mitochondrial susceptibility. Present study investigated the mitochondrial impairments with implicated cell death upon DBP exposure on zebrafish cells. Elevated mitochondrial oxidative stress reduced its membrane potential and count, enhanced fragmentation, and impaired ultrastructure that showed smaller size and cristae rupture. Afterwards, the critical function of ATP synthesis was damaged and the stabilized binding capacity between DBP with mitochondrial respiratory complexes was simulated by the molecular docking. And the top pathways enrichment of mitochondrion and metabolism by transcriptome analyses verified the mitochondrial dysfunction that indicated the human diseases risks. The mitochondrial DNA (mtDNA) replication and transcription with DNA methylation modifications were also disrupted, reflecting the genotoxicity on mtDNA. Moreover, the activated autophagy and apoptosis underlying mitochondrial susceptibility integrated into cellular homeostasis changes. These findings provide the first systemic evidence broadening and illustrating the mitochondrial toxicity of DBP exposure on zebrafish model that raise concern on phthalates contamination and ecotoxicological evaluation.
Collapse
Affiliation(s)
- Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Dingfu Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tingting Hou
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qianqing Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| |
Collapse
|
25
|
Kong Y, Mead EA, Fang G. Navigating the pitfalls of mapping DNA and RNA modifications. Nat Rev Genet 2023; 24:363-381. [PMID: 36653550 PMCID: PMC10722219 DOI: 10.1038/s41576-022-00559-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/21/2022] [Indexed: 01/19/2023]
Abstract
Chemical modifications to nucleic acids occur across the kingdoms of life and carry important regulatory information. Reliable high-resolution mapping of these modifications is the foundation of functional and mechanistic studies, and recent methodological advances based on next-generation sequencing and long-read sequencing platforms are critical to achieving this aim. However, mapping technologies may have limitations that sometimes lead to inconsistent results. Some of these limitations are technical in nature and specific to certain types of technology. Here, however, we focus on common (yet not always widely recognized) pitfalls that are shared among frequently used mapping technologies and discuss strategies to help technology developers and users mitigate their effects. Although the emphasis is primarily on DNA modifications, RNA modifications are also discussed.
Collapse
Affiliation(s)
- Yimeng Kong
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edward A Mead
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Gang Fang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
26
|
Casanova A, Wevers A, Navarro-Ledesma S, Pruimboom L. Mitochondria: It is all about energy. Front Physiol 2023; 14:1114231. [PMID: 37179826 PMCID: PMC10167337 DOI: 10.3389/fphys.2023.1114231] [Citation(s) in RCA: 39] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/29/2023] [Indexed: 05/15/2023] Open
Abstract
Mitochondria play a key role in both health and disease. Their function is not limited to energy production but serves multiple mechanisms varying from iron and calcium homeostasis to the production of hormones and neurotransmitters, such as melatonin. They enable and influence communication at all physical levels through interaction with other organelles, the nucleus, and the outside environment. The literature suggests crosstalk mechanisms between mitochondria and circadian clocks, the gut microbiota, and the immune system. They might even be the hub supporting and integrating activity across all these domains. Hence, they might be the (missing) link in both health and disease. Mitochondrial dysfunction is related to metabolic syndrome, neuronal diseases, cancer, cardiovascular and infectious diseases, and inflammatory disorders. In this regard, diseases such as cancer, Alzheimer's, Parkinson's, amyotrophic lateral sclerosis (ALS), chronic fatigue syndrome (CFS), and chronic pain are discussed. This review focuses on understanding the mitochondrial mechanisms of action that allow for the maintenance of mitochondrial health and the pathways toward dysregulated mechanisms. Although mitochondria have allowed us to adapt to changes over the course of evolution, in turn, evolution has shaped mitochondria. Each evolution-based intervention influences mitochondria in its own way. The use of physiological stress triggers tolerance to the stressor, achieving adaptability and resistance. This review describes strategies that could recover mitochondrial functioning in multiple diseases, providing a comprehensive, root-cause-focused, integrative approach to recovering health and treating people suffering from chronic diseases.
Collapse
Affiliation(s)
- Amaloha Casanova
- Department of Physiotherapy, University of Granada, Granada, Spain
- Faculty of Health Sciences, Melilla, Spain
- PNI Europe, The Hague, Netherlands
- Chair of Clinical Psychoneuroimmunology, University of Granada and PNI Europe, Granada, Spain
| | - Anne Wevers
- Department of Physiotherapy, University of Granada, Granada, Spain
- Faculty of Health Sciences, Melilla, Spain
- PNI Europe, The Hague, Netherlands
- Chair of Clinical Psychoneuroimmunology, University of Granada and PNI Europe, Granada, Spain
| | - Santiago Navarro-Ledesma
- Department of Physiotherapy, University of Granada, Granada, Spain
- Faculty of Health Sciences, Melilla, Spain
- PNI Europe, The Hague, Netherlands
- Chair of Clinical Psychoneuroimmunology, University of Granada and PNI Europe, Granada, Spain
| | - Leo Pruimboom
- PNI Europe, The Hague, Netherlands
- Chair of Clinical Psychoneuroimmunology, University of Granada and PNI Europe, Granada, Spain
| |
Collapse
|
27
|
Shukla P, Melkani GC. Mitochondrial epigenetic modifications and nuclear-mitochondrial communication: A new dimension towards understanding and attenuating the pathogenesis in women with PCOS. Rev Endocr Metab Disord 2023; 24:317-326. [PMID: 36705802 PMCID: PMC10150397 DOI: 10.1007/s11154-023-09789-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/16/2023] [Indexed: 01/28/2023]
Abstract
Mitochondrial DNA (mtDNA) epigenetic modifications have recently gained attention in a plethora of complex diseases, including polycystic ovary syndrome (PCOS), a common cause of infertility in women of reproductive age. Herein we discussed mtDNA epigenetic modifications and their impact on nuclear-mitochondrial interactions in general and the latest advances indicating the role of mtDNA methylation in the pathophysiology of PCOS. We highlighted epigenetic changes in nuclear-related mitochondrial genes, including nuclear transcription factors that regulate mitochondrial function and may be involved in the development of PCOS or its related traits. Additionally, therapies targeting mitochondrial epigenetics, including time-restricted eating (TRE), which has been shown to have beneficial effects by improving mitochondrial function and may be mediated by epigenetic modifications, have also been discussed. As PCOS has become a major metabolic disorder and a risk factor for obesity, cardiometabolic disorders, and diabetes, lifestyle/behavior intervention using TRE that reinforces feeding-fasting rhythms without reducing caloric intake may be a promising therapeutic strategy for attenuating the pathogenesis. Furthermore, future perspectives in the area of mitochondrial epigenetics are described.
Collapse
Affiliation(s)
- Pallavi Shukla
- Department of Molecular Endocrinology, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health (ICMR-NIRRCH), J.M. Street, Parel, Mumbai, 400012, India.
| | - Girish C Melkani
- Department of Pathology, Division of Molecular and Cellular Pathology, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35294, United States
| |
Collapse
|
28
|
Ji S, Xiong M, Chen H, Liu Y, Zhou L, Hong Y, Wang M, Wang C, Fu X, Sun X. Cellular rejuvenation: molecular mechanisms and potential therapeutic interventions for diseases. Signal Transduct Target Ther 2023; 8:116. [PMID: 36918530 PMCID: PMC10015098 DOI: 10.1038/s41392-023-01343-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 12/16/2022] [Accepted: 01/19/2023] [Indexed: 03/16/2023] Open
Abstract
The ageing process is a systemic decline from cellular dysfunction to organ degeneration, with more predisposition to deteriorated disorders. Rejuvenation refers to giving aged cells or organisms more youthful characteristics through various techniques, such as cellular reprogramming and epigenetic regulation. The great leaps in cellular rejuvenation prove that ageing is not a one-way street, and many rejuvenative interventions have emerged to delay and even reverse the ageing process. Defining the mechanism by which roadblocks and signaling inputs influence complex ageing programs is essential for understanding and developing rejuvenative strategies. Here, we discuss the intrinsic and extrinsic factors that counteract cell rejuvenation, and the targeted cells and core mechanisms involved in this process. Then, we critically summarize the latest advances in state-of-art strategies of cellular rejuvenation. Various rejuvenation methods also provide insights for treating specific ageing-related diseases, including cellular reprogramming, the removal of senescence cells (SCs) and suppression of senescence-associated secretory phenotype (SASP), metabolic manipulation, stem cells-associated therapy, dietary restriction, immune rejuvenation and heterochronic transplantation, etc. The potential applications of rejuvenation therapy also extend to cancer treatment. Finally, we analyze in detail the therapeutic opportunities and challenges of rejuvenation technology. Deciphering rejuvenation interventions will provide further insights into anti-ageing and ageing-related disease treatment in clinical settings.
Collapse
Affiliation(s)
- Shuaifei Ji
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Mingchen Xiong
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Huating Chen
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Yiqiong Liu
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Laixian Zhou
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Yiyue Hong
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Mengyang Wang
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China
| | - Chunming Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, 999078, Macau SAR, China.
| | - Xiaobing Fu
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China.
| | - Xiaoyan Sun
- Research Center for Tissue Repair and Regeneration Affiliated to Medical Innovation Research Department and 4th Medical Center, PLA General Hospital and PLA Medical College; PLA Key Laboratory of Tissue Repair and Regenerative Medicine and Beijing Key Research Laboratory of Skin Injury, Repair and Regeneration; Research Unit of Trauma Care, Tissue Repair and Regeneration, Chinese Academy of Medical Sciences, 2019RU051, Beijing, 100048, P. R. China.
| |
Collapse
|
29
|
Molinero N, Antón-Fernández A, Hernández F, Ávila J, Bartolomé B, Moreno-Arribas MV. Gut Microbiota, an Additional Hallmark of Human Aging and Neurodegeneration. Neuroscience 2023; 518:141-161. [PMID: 36893982 DOI: 10.1016/j.neuroscience.2023.02.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 02/10/2023] [Accepted: 02/19/2023] [Indexed: 03/09/2023]
Abstract
Gut microbiota represents a diverse and dynamic population of microorganisms harbouring the gastrointestinal tract, which influences host health and disease. Bacterial colonization of the gastrointestinal tract begins at birth and changes throughout life, with age being one of the conditioning factors for its vitality. Aging is also a primary risk factor for most neurodegenerative diseases. Among them, Alzheimeŕs disease (AD) is probably the one where its association with a state of dysbiosis of the gut microbiota has been most studied. In particular, intestinal microbial-derived metabolites have been associated with β-amyloid formation and brain amyloid deposition, tau phosphorylation, as well as neuroinflammation in AD patients. Moreover, it has been suggested that some oral bacteria increase the risk of developing AD. However, the causal connections among microbiome, amyloid-tau interaction, and neurodegeneration need to be addressed. This paper summarizes the emerging evidence in the literature regarding the link between the oral and gut microbiome and neurodegeneration with a focus on AD. Taxonomic features of bacteria as well as microbial functional alterations associated with AD biomarkers are the main points reviewed. Data from clinical studies as well as the link between microbiome and clinical determinants of AD are particularly emphasized. Further, relationships between gut microbiota and age-dependent epigenetic changes and other neurological disorders are also described. Together, all this evidence suggests that, in some sense, gut microbiota can be seen as an additional hallmark of human aging and neurodegeneration.
Collapse
Affiliation(s)
- Natalia Molinero
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM. c/ Nicolás Cabrera, 9. 28049 Madrid, Spain
| | - Alejandro Antón-Fernández
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM. c/ Nicolás Cabrera, 1. 28049 Madrid, Spain
| | - Félix Hernández
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM. c/ Nicolás Cabrera, 1. 28049 Madrid, Spain
| | - Jesús Ávila
- Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC-UAM. c/ Nicolás Cabrera, 1. 28049 Madrid, Spain
| | - Begoña Bartolomé
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM. c/ Nicolás Cabrera, 9. 28049 Madrid, Spain
| | - M Victoria Moreno-Arribas
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM. c/ Nicolás Cabrera, 9. 28049 Madrid, Spain.
| |
Collapse
|
30
|
Salemi M, Ridolfo F, Salluzzo MG, Schillaci FA, Caniglia S, Lanuzza B, Cantone M, Ferri R. Humanin gene expression in subjects with Parkinson's disease. Mol Biol Rep 2023; 50:2943-2949. [PMID: 36626066 DOI: 10.1007/s11033-022-08132-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/16/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Bradykinesia, tremor, rigidity and postural instability are the hallmark of Parkinson's disease (PD). Non-motor symptoms including cognitive, behavioral, and neuropsychiatric changes, sensory and sleep disturbances that may precede the motor symptoms by years. The peculiar pathological features of PD are decreased dopaminergic neurons and dopamine levels in the substantia nigra pars compacta and pontine locus coeruleus. Humanin is produced by a small gene peptide, which is located in the mitochondria genome. Inflammation, oxidative stress, mitochondrial dysfunction and altered transcription have been recognized as causative factors of PD. This evidence has prompted many researchers to focus on studying the functions of DNA and mitochondria. The purpose of the present study was to evaluate Humanin mRNA levels in peripheral blood mononuclear cells (PBMCs) of PD subjects, compared with those in PBMCs of normal control (NC) subjects. METHODS AND RESULTS A total of 220 participants, including 154 PD patients (57 females and 97 males; mean age 71.54 years, SD 7.8) and 66 CN (28 females and 38 males; mean age 70.54 years, SD 9.45) were enrolled for the qRT-PCR analysis. Increased Humanin mRNA levels were found in PD samples, compared to controls. CONCLUSION In conclusion, the present data confirm the tendency of mitochondria to overexpress mRNA in PD, which could be a cellular attempt to reduce apoptotic damage in PD subjects. Humanin might be useful as a marker for a better diagnosis of PD, and we cannot exclude that in the future it might also play a role on prognosis and in the possible therapies for PD.
Collapse
Affiliation(s)
| | - Federico Ridolfo
- UOC of Clinical Pathology, ASUR Marche -AV4, Hospital of Fermo, Fermo, Italy
| | | | | | | | | | - Mariagiovanna Cantone
- Neurology Unit, University Hospital Policlinico "G.Rodolico-San Marco", Catania, Italy
| | | |
Collapse
|
31
|
Dong LF, Rohlena J, Zobalova R, Nahacka Z, Rodriguez AM, Berridge MV, Neuzil J. Mitochondria on the move: Horizontal mitochondrial transfer in disease and health. J Cell Biol 2023; 222:213873. [PMID: 36795453 PMCID: PMC9960264 DOI: 10.1083/jcb.202211044] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/12/2023] [Accepted: 02/01/2023] [Indexed: 02/17/2023] Open
Abstract
Mammalian genes were long thought to be constrained within somatic cells in most cell types. This concept was challenged recently when cellular organelles including mitochondria were shown to move between mammalian cells in culture via cytoplasmic bridges. Recent research in animals indicates transfer of mitochondria in cancer and during lung injury in vivo, with considerable functional consequences. Since these pioneering discoveries, many studies have confirmed horizontal mitochondrial transfer (HMT) in vivo, and its functional characteristics and consequences have been described. Additional support for this phenomenon has come from phylogenetic studies. Apparently, mitochondrial trafficking between cells occurs more frequently than previously thought and contributes to diverse processes including bioenergetic crosstalk and homeostasis, disease treatment and recovery, and development of resistance to cancer therapy. Here we highlight current knowledge of HMT between cells, focusing primarily on in vivo systems, and contend that this process is not only (patho)physiologically relevant, but also can be exploited for the design of novel therapeutic approaches.
Collapse
Affiliation(s)
- Lan-Feng Dong
- https://ror.org/02sc3r913School of Pharmacy and Medical Sciences, Griffith University, Southport, Australia,Lan-Feng Dong:
| | - Jakub Rohlena
- https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic
| | - Renata Zobalova
- https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic
| | - Zuzana Nahacka
- https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic
| | | | | | - Jiri Neuzil
- https://ror.org/02sc3r913School of Pharmacy and Medical Sciences, Griffith University, Southport, Australia,https://ror.org/00wzqmx94Institute of Biotechnology, Academy of Sciences of the Czech Republic, Prague-West, Czech Republic,Faculty of Science, Charles University, Prague, Czech Republic,First Faculty of Medicine, Charles University, Prague, Czech Republic,Correspondence to Jiri Neuzil: ,
| |
Collapse
|
32
|
Rehman A, Kumari R, Kamthan A, Tiwari R, Srivastava RK, van der Westhuizen FH, Mishra PK. Cell-free circulating mitochondrial DNA: An emerging biomarker for airborne particulate matter associated with cardiovascular diseases. Free Radic Biol Med 2023; 195:103-120. [PMID: 36584454 DOI: 10.1016/j.freeradbiomed.2022.12.083] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022]
Abstract
The association of airborne particulate matter exposure with the deteriorating function of the cardiovascular system is fundamentally driven by the impairment of mitochondrial-nuclear crosstalk orchestrated by aberrant redox signaling. The loss of delicate balance in retrograde communication from mitochondria to the nucleus often culminates in the methylation of the newly synthesized strand of mitochondrial DNA (mtDNA) through DNA methyl transferases. In highly metabolic active tissues such as the heart, mtDNA's methylation state alteration impacts mitochondrial bioenergetics. It affects transcriptional regulatory processes involved in biogenesis, fission, and fusion, often accompanied by the integrated stress response. Previous studies have demonstrated a paradoxical role of mtDNA methylation in cardiovascular pathologies linked to air pollution. A pronounced alteration in mtDNA methylation contributes to systemic inflammation, an etiological determinant for several co-morbidities, including vascular endothelial dysfunction and myocardial injury. In the current article, we evaluate the state of evidence and examine the considerable promise of using cell-free circulating methylated mtDNA as a predictive biomarker to reduce the more significant burden of ambient air pollution on cardiovascular diseases.
Collapse
Affiliation(s)
- Afreen Rehman
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| | - Roshani Kumari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| | - Arunika Kamthan
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| | - Rajnarayan Tiwari
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| | | | | | - Pradyumna Kumar Mishra
- Department of Molecular Biology, ICMR-National Institute for Research in Environmental Health, Bhopal, India.
| |
Collapse
|
33
|
High-fructose corn syrup intake increases hepatic mitochondrial DNA copy number and methylation in adolescent rats. Nutr Res 2023; 110:57-65. [PMID: 36682228 DOI: 10.1016/j.nutres.2022.12.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 12/14/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022]
Abstract
High-fructose corn syrup (HFCS) is consumed worldwide. However, it has been demonstrated that an increased intake of sweetened beverages, including those sweetened using fructose, is associated with the development of childhood obesity. It is unknown why the negative effects of fructose are stronger in young persons than in elderly individuals. In recent years, mitochondria have been identified as 1 of the targets of the negative effects of fructose; they possess their own genome called mitochondrial DNA (mtDNA), which encodes genes involved in metabolic functions. We hypothesized that HFCS intake affects mtDNA in the livers of rats, and that the intensity of these effects is age-dependent. The experimental period was divided into 3 parts: childhood and adolescence (postnatal day [PD] 21-60), young adulthood (PD61-100), and adulthood (PD101-140). Rats in the different age groups were assigned to receive either water (control group [CONT]) or a 20% HFCS solution (HFCS). The hepatic mtDNA copy number of the HFCS group was higher than that of the CONT group in childhood and adolescence. In addition, the mtDNA methylation level was increased in the HFCS group in the same experimental period. No significant differences were observed between the CONT and HFCS groups during the other experimental periods. We demonstrated that HFCS has the strongest effect on mtDNA during childhood and adolescence, suggesting a need to analyze the HFCS intake of young people.
Collapse
|
34
|
Naren P, Cholkar A, Kamble S, Khan SS, Srivastava S, Madan J, Mehra N, Tiwari V, Singh SB, Khatri DK. Pathological and Therapeutic Advances in Parkinson's Disease: Mitochondria in the Interplay. J Alzheimers Dis 2023; 94:S399-S428. [PMID: 36093711 PMCID: PMC10473111 DOI: 10.3233/jad-220682] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2022] [Indexed: 11/15/2022]
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative illness majorly affecting the population between the ages of 55 to 65 years. Progressive dopaminergic neuronal loss and the collective assemblage of misfolded alpha-synuclein in the substantia nigra, remain notable neuro-pathological hallmarks of the disease. Multitudes of mechanistic pathways have been proposed in attempts to unravel the pathogenesis of PD but still, it remains elusive. The convergence of PD pathology is found in organelle dysfunction where mitochondria remain a major contributor. Mitochondrial processes like bioenergetics, mitochondrial dynamics, and mitophagy are under strict regulation by the mitochondrial genome and nuclear genome. These processes aggravate neurodegenerative activities upon alteration through neuroinflammation, oxidative damage, apoptosis, and proteostatic stress. Therefore, the mitochondria have grabbed a central position in the patho-mechanistic exploration of neurodegenerative diseases like PD. The management of PD remains a challenge to physicians to date, due to the variable therapeutic response of patients and the limitation of conventional chemical agents which only offer symptomatic relief with minimal to no disease-modifying effect. This review describes the patho-mechanistic pathways involved in PD not only limited to protein dyshomeostasis and oxidative stress, but explicit attention has been drawn to exploring mechanisms like organelle dysfunction, primarily mitochondria and mitochondrial genome influence, while delineating the newer exploratory targets such as GBA1, GLP, LRRK2, and miRNAs and therapeutic agents targeting them.
Collapse
Affiliation(s)
- Padmashri Naren
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Anjali Cholkar
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Suchita Kamble
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Sabiya Samim Khan
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Saurabh Srivastava
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana, India
| | - Jitender Madan
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana, India
| | - Neelesh Mehra
- Department of Pharmaceutics, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Telangana, India
| | - Vinod Tiwari
- Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (B.H.U.) Varanasi (U.P.), India
| | - Shashi Bala Singh
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Dharmendra Kumar Khatri
- Department of Pharmacology & Toxicology, National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| |
Collapse
|
35
|
Cai Z, Liu M, Zeng L, Zhao K, Wang C, Sun T, Li Z, Liu R. Role of traditional Chinese medicine in ameliorating mitochondrial dysfunction via non-coding RNA signaling: Implication in the treatment of neurodegenerative diseases. Front Pharmacol 2023; 14:1123188. [PMID: 36937876 PMCID: PMC10014574 DOI: 10.3389/fphar.2023.1123188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/17/2023] [Indexed: 03/05/2023] Open
Abstract
Neurodegenerative diseases (NDs) are common chronic disorders associated with progressive nervous system damage, including Alzheimer's disease, Parkinson's disease, and Huntington's disease, among others. Mitochondria are abundant in various nervous system cells and provide a bulk supply of the adenosine triphosphate necessary for brain function, considered the center of the free-radical theory of aging. One common feature of NDs is mitochondrial dysfunction, which is involved in many physiopathological processes, including apoptosis, inflammation, oxidative stress, and calcium homeostasis. Recently, genetic studies revealed extensive links between mitochondrion impairment and dysregulation of non-coding RNAs (ncRNAs) in the pathology of NDs. Traditional Chinese medicines (TCMs) have been used for thousands of years in treating NDs. Numerous modern pharmacological studies have demonstrated the therapeutic effects of prescription, herbal medicine, bioactive ingredients, and monomer compounds of TCMs, which are important for managing the symptoms of NDs. Some highly effective TCMs exert protective effects on various key pathological features regulated by mitochondria and play a pivotal role in recovering disrupted signaling pathways. These disrupted signaling pathways are induced by abnormally-expressed ncRNAs associated with mitochondrial dysfunction, including microRNAs, long ncRNAs, and circular RNAs. In this review, we first explored the underlying ncRNA mechanisms linking mitochondrial dysfunction and neurodegeneration, demonstrating the implication of ncRNA-induced mitochondrial dysfunction in the pathogenesis of NDs. The ncRNA-induced mitochondrial dysfunctions affect mitochondrial biogenesis, dynamics, autophagy, Ca2+ homeostasis, oxidative stress, and downstream apoptosis. The review also discussed the targeting of the disease-related mitochondrial proteins in NDs and the protective effects of TCM formulas with definite composition, standardized extracts from individual TCMs, and monomeric compounds isolated from TCM. Additionally, we explored the ncRNA regulation of mitochondrial dysfunction in NDs and the effects and potential mechanisms of representative TCMs in alleviating mitochondrial pathogenesis and conferring anti-inflammatory, antioxidant, and anti-apoptotic pathways against NDs. Therefore, this review presents an overview of the role of mitochondrion-related ncRNAs and the target genes for TCM-based therapeutic interventions in NDs, providing insight into understanding the "multi-level compound-target-pathway regulatory" treatment mechanism of TCMs.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Rui Liu
- *Correspondence: Zhuorong Li, ; Rui Liu,
| |
Collapse
|
36
|
King DE, Sparling AC, Lloyd D, Satusky MJ, Martinez M, Grenier C, Bergemann CM, Maguire R, Hoyo C, Meyer JN, Murphy SK. Sex-specific DNA methylation and associations with in utero tobacco smoke exposure at nuclear-encoded mitochondrial genes. Epigenetics 2022; 17:1573-1589. [PMID: 35238269 PMCID: PMC9620986 DOI: 10.1080/15592294.2022.2043591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Sex-linked differences in mitochondrial ATP production, enzyme activities, and reactive oxygen species generation have been reported in multiple tissue and cell types. While the effects of reproductive hormones underlie many of these differences, regulation of sexually dimorphic mitochondrial function has not been fully characterized. We hypothesized that sex-specific DNA methylation contributes to sex-specific expression of nuclear genes that influence mitochondrial function. Herein, we analysed DNA methylation data specifically focused on nuclear-encoded mitochondrial genes in 191 males and 190 females. We found 596 differentially methylated sites (DMSs) (FDR p < 0.05), corresponding to 324 genes, with at least a 1% difference in methylation between sexes. To investigate the potential functional significance, we utilized gene expression microarray data. Of the 324 genes containing DMSs, 17 showed differences in gene expression by sex. Particularly striking was that ATP5G2, encoding subunit C of ATP synthase, contains seven DMSs and exhibits a sex difference in expression (p = 0.04). Finally, we also found that alterations in DNA methylation associated with in utero tobacco smoke exposure were sex-specific in these nuclear-encoded mitochondrial genes. Interestingly, the level of sex differences in DNA methylation at nuclear-encoded mitochondrial genes and the level of methylation changes associated with smoke exposure were less prominent than that of other genes. This suggests more conservative regulation of DNA methylation at these nuclear-encoded mitochondrial genes as compared to others. Overall, our findings suggest that sex-specific DNA methylation may help establish sex differences in expression and function and that sex-specific alterations in DNA methylation in response to exposures could contribute to sex-variable toxicological responses.
Collapse
Affiliation(s)
- Dillon E. King
- Nicholas School of the Environment, Duke University, Durham, NC, USA,Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Anna Clare Sparling
- Nicholas School of the Environment, Duke University, Durham, NC, USA,Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Dillon Lloyd
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Matthew Joseph Satusky
- Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Mackenzie Martinez
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | - Carole Grenier
- Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA
| | | | - Rachel Maguire
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Cathrine Hoyo
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Joel Newman Meyer
- Nicholas School of the Environment, Duke University, Durham, NC, USA
| | - Susan K. Murphy
- Nicholas School of the Environment, Duke University, Durham, NC, USA,Department of Obstetrics and Gynecology, Duke University Medical Center, Durham, NC, USA,CONTACT Susan K. Murphy 701 W. Main Street, Suite 510, Durham, NC27701, USA Department of Obstetrics and Gynecology, Duke University Medical Center
| |
Collapse
|
37
|
Wang Z, Zheng H, Huang J, Yang G, Yan K, Zhang S, Wu C, Zheng C. DEMETHYLATION REGULATOR 1 regulates DNA demethylation of the nuclear and mitochondrial genomes. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2344-2360. [PMID: 36223079 DOI: 10.1111/jipb.13386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Active DNA demethylation effectively modulates gene expression during plant development and in response to stress. However, little is known about the upstream regulatory factors that regulate DNA demethylation. We determined that the demethylation regulator 1 (demr1) mutant exhibits a distinct DNA methylation profile at selected loci queried by methylation-sensitive polymerase chain reaction and globally based on whole-genome bisulfite sequencing. Notably, the transcript levels of the DNA demethylase gene REPRESSOR OF SILENCING 1 (ROS1) were lower in the demr1 mutant. We established that DEMR1 directly binds to the ROS1 promoter in vivo and in vitro, and the methylation level in the DNA methylation monitoring sequence of ROS1 promoter decreased by 60% in the demr1 mutant. About 40% of the hyper-differentially methylated regions (DMRs) in the demr1 mutant were shared with the ros1-4 mutant. Genetic analysis indicated that DEMR1 acts upstream of ROS1 to positively regulate abscisic acid (ABA) signaling during seed germination and seedling establishment stages. Surprisingly, the loss of DEMR1 function also caused a rise in methylation levels of the mitochondrial genome, impaired mitochondrial structure and an early flowering phenotype. Together, our results show that DEMR1 is a novel regulator of DNA demethylation of both the nuclear and mitochondrial genomes in response to ABA and plant development in Arabidopsis.
Collapse
Affiliation(s)
- Zhen Wang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Hao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
- National Institute of Biological Sciences (NIBS), Beijing, 102206, China
| | - Jinguang Huang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Guodong Yang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Shizhong Zhang
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Changai Wu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| | - Chengchao Zheng
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China
| |
Collapse
|
38
|
Szukiewicz D, Trojanowski S, Kociszewska A, Szewczyk G. Modulation of the Inflammatory Response in Polycystic Ovary Syndrome (PCOS)-Searching for Epigenetic Factors. Int J Mol Sci 2022; 23:ijms232314663. [PMID: 36498989 PMCID: PMC9736994 DOI: 10.3390/ijms232314663] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/19/2022] [Accepted: 11/21/2022] [Indexed: 11/25/2022] Open
Abstract
Polycystic ovary syndrome (PCOS) is the most common endocrine disorder in women of reproductive age. Despite its incidence, the syndrome is poorly understood and remains underdiagnosed, and female patients are diagnosed with a delay. The heterogenous nature of this complex disorder results from the combined occurrence of genetic, environmental, endocrine, and behavioral factors. Primary clinical manifestations of PCOS are derived from the excess of androgens (anovulation, polycystic ovary morphology, lack of or scanty, irregular menstrual periods, acne and hirsutism), whereas the secondary manifestations include multiple metabolic, cardiovascular, and psychological disorders. Dietary and lifestyle factors play important roles in the development and course of PCOS, which suggests strong epigenetic and environmental influences. Many studies have shown a strong association between PCOS and chronic, low-grade inflammation both in the ovarian tissue and throughout the body. In the vast majority of PCOS patients, elevated values of inflammatory markers or their gene markers have been reported. Development of the vicious cycle of the chronic inflammatory state in PCOS is additionally stimulated by hyperinsulinemia and obesity. Changes in DNA methylation, histone acetylation and noncoding RNA levels are presented in this review in the context of oxidative stress, reactive oxygen species, and inflammatory signaling in PCOS. Epigenetic modulation of androgenic activity in response to inflammatory signaling is also discussed.
Collapse
Affiliation(s)
- Dariusz Szukiewicz
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, 02-004 Warsaw, Poland
- Correspondence:
| | - Seweryn Trojanowski
- Chair and Department of Obstetrics, Gynecology and Gynecological Oncology, Medical University of Warsaw, 03-242 Warsaw, Poland
| | - Anna Kociszewska
- Chair and Department of Obstetrics, Gynecology and Gynecological Oncology, Medical University of Warsaw, 03-242 Warsaw, Poland
| | - Grzegorz Szewczyk
- Department of Biophysics, Physiology & Pathophysiology, Faculty of Health Sciences, Medical University of Warsaw, 02-004 Warsaw, Poland
| |
Collapse
|
39
|
Bai J, Wu L, Wang X, Wang Y, Shang Z, Jiang E, Shao Z. Roles of Mitochondria in Oral Squamous Cell Carcinoma Therapy: Friend or Foe? Cancers (Basel) 2022; 14:cancers14235723. [PMID: 36497206 PMCID: PMC9738284 DOI: 10.3390/cancers14235723] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 11/24/2022] Open
Abstract
Oral squamous cell carcinoma (OSCC) therapy is unsatisfactory, and the prevalence of the disease is increasing. The role of mitochondria in OSCC therapy has recently attracted increasing attention, however, many mechanisms remain unclear. Therefore, we elaborate upon relative studies in this review to achieve a better therapeutic effect of OSCC treatment in the future. Interestingly, we found that mitochondria not only contribute to OSCC therapy but also promote resistance, and targeting the mitochondria of OSCC via nanoparticles is a promising way to treat OSCC.
Collapse
Affiliation(s)
- Junqiang Bai
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM), School & Hospital of Stomatology, Wuhan University, Wuhan 430089, China
| | - Luping Wu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM), School & Hospital of Stomatology, Wuhan University, Wuhan 430089, China
| | - Xinmiao Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM), School & Hospital of Stomatology, Wuhan University, Wuhan 430089, China
| | - Yifan Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM), School & Hospital of Stomatology, Wuhan University, Wuhan 430089, China
| | - Zhengjun Shang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM), School & Hospital of Stomatology, Wuhan University, Wuhan 430089, China
- Department of Oral and Maxillofacial-Head and Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan 430089, China
| | - Erhui Jiang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM), School & Hospital of Stomatology, Wuhan University, Wuhan 430089, China
- Department of Oral and Maxillofacial-Head and Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan 430089, China
- Correspondence: (E.J.); (Z.S.); Tel.: +86-27-87686215 (E.J. & Z.S.)
| | - Zhe Shao
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education (KLOBM), School & Hospital of Stomatology, Wuhan University, Wuhan 430089, China
- Department of Oral and Maxillofacial-Head and Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan 430089, China
- Correspondence: (E.J.); (Z.S.); Tel.: +86-27-87686215 (E.J. & Z.S.)
| |
Collapse
|
40
|
Andrawus M, Sharvit L, Atzmon G. Epigenetics and Pregnancy: Conditional Snapshot or Rolling Event. Int J Mol Sci 2022; 23:12698. [PMID: 36293556 PMCID: PMC9603966 DOI: 10.3390/ijms232012698] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/12/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
Epigenetics modification such as DNA methylation can affect maternal health during the gestation period. Furthermore, pregnancy can drive a range of physiological and molecular changes that have the potential to contribute to pathological conditions. Pregnancy-related risk factors include multiple environmental, behavioral, and hereditary factors that can impact maternal DNA methylation with long-lasting consequences. Identification of the epigenetic patterns linked to poor pregnancy outcomes is crucial since changes in DNA methylation patterns can have long-term effects. In this review, we provide an overview of the epigenetic changes that influence pregnancy-related molecular programming such as gestational diabetes, immune response, and pre-eclampsia, in an effort to close the gap in current understanding regarding interactions between the environment, the genetics of the fetus, and the pregnant woman.
Collapse
Affiliation(s)
| | | | - Gil Atzmon
- Department of Human Biology, University of Haifa, Haifa 3498838, Israel
| |
Collapse
|
41
|
Marmolejo-Garza A, Medeiros-Furquim T, Rao R, Eggen BJL, Boddeke E, Dolga AM. Transcriptomic and epigenomic landscapes of Alzheimer's disease evidence mitochondrial-related pathways. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119326. [PMID: 35839870 DOI: 10.1016/j.bbamcr.2022.119326] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 07/06/2022] [Accepted: 07/07/2022] [Indexed: 02/06/2023]
Abstract
Alzheimers disease (AD) is the main cause of dementia and it is defined by cognitive decline coupled to extracellular deposit of amyloid-beta protein and intracellular hyperphosphorylation of tau protein. Historically, efforts to target such hallmarks have failed in numerous clinical trials. In addition to these hallmark-targeted approaches, several clinical trials focus on other AD pathological processes, such as inflammation, mitochondrial dysfunction, and oxidative stress. Mitochondria and mitochondrial-related mechanisms have become an attractive target for disease-modifying strategies, as mitochondrial dysfunction prior to clinical onset has been widely described in AD patients and AD animal models. Mitochondrial function relies on both the nuclear and mitochondrial genome. Findings from omics technologies have shed light on AD pathophysiology at different levels (e.g., epigenome, transcriptome and proteome). Most of these studies have focused on the nuclear-encoded components. The first part of this review provides an updated overview of the mechanisms that regulate mitochondrial gene expression and function. The second part of this review focuses on evidence of mitochondrial dysfunction in AD. We have focused on published findings and datasets that study AD. We analyzed published data and provide examples for mitochondrial-related pathways. These pathways are strikingly dysregulated in AD neurons and glia in sex-, cell- and disease stage-specific manners. Analysis of mitochondrial omics data highlights the involvement of mitochondria in AD, providing a rationale for further disease modeling and drug targeting.
Collapse
Affiliation(s)
- Alejandro Marmolejo-Garza
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands; Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Tiago Medeiros-Furquim
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands; Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Ramya Rao
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands
| | - Bart J L Eggen
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Erik Boddeke
- Department of Biomedical Sciences of Cells & Systems, Section Molecular Neurobiology, Faculty of Medical Sciences, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands; Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen N, Denmark.
| | - Amalia M Dolga
- Department of Molecular Pharmacology, Faculty of Science and Engineering, Groningen Research Institute of Pharmacy (GRIP), University of Groningen, the Netherlands.
| |
Collapse
|
42
|
Targeted Mitochondrial Epigenetics: A New Direction in Alzheimer’s Disease Treatment. Int J Mol Sci 2022; 23:ijms23179703. [PMID: 36077101 PMCID: PMC9456144 DOI: 10.3390/ijms23179703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/19/2022] [Accepted: 08/25/2022] [Indexed: 11/23/2022] Open
Abstract
Mitochondrial epigenetic alterations are closely related to Alzheimer’s disease (AD), which is described in this review. Reports of the alteration of mitochondrial DNA (mtDNA) methylation in AD demonstrate that the disruption of the dynamic balance of mtDNA methylation and demethylation leads to damage to the mitochondrial electron transport chain and the obstruction of mitochondrial biogenesis, which is the most studied mitochondrial epigenetic change. Mitochondrial noncoding RNA modifications and the post-translational modification of mitochondrial nucleoproteins have been observed in neurodegenerative diseases and related diseases that increase the risk of AD. Although there are still relatively few mitochondrial noncoding RNA modifications and mitochondrial nuclear protein post-translational modifications reported in AD, we have reason to believe that these mitochondrial epigenetic modifications also play an important role in the AD process. This review provides a new research direction for the AD mechanism, starting from mitochondrial epigenetics. Further, this review summarizes therapeutic approaches to targeted mitochondrial epigenetics, which is the first systematic summary of therapeutic approaches in the field, including folic acid supplementation, mitochondrial-targeting antioxidants, and targeted ubiquitin-specific proteases, providing a reference for therapeutic targets for AD.
Collapse
|
43
|
Sanyal T, Das A, Bhowmick P, Bhattacharjee P. Interplay between environmental exposure and mitochondrial DNA methylation in disease susceptibility and cancer: a comprehensive review. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00392-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
|
44
|
Erturk E, Enes Onur O, Akgun O, Tuna G, Yildiz Y, Ari F. Mitochondrial miRNAs (MitomiRs): Their potential roles in breast and other cancers. Mitochondrion 2022; 66:74-81. [PMID: 35963496 DOI: 10.1016/j.mito.2022.08.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/19/2022] [Accepted: 08/02/2022] [Indexed: 11/15/2022]
Abstract
Breast cancer is the most common cancer in women worldwide. MicroRNAs (miRNAs) are non-coding RNAs that are involved in the post-transcriptional regulation of gene expression. Although miRNAs mainly act in the cytoplasm, they can be found in the mitochondrial compartment of the cell. These miRNAs called "MitomiR", they can change mitochondrial functions by regulating proteins at the mitochondrial level and cause cancer. In this review, we have aimed to explain miRNA biogenesis, transport pathways to mitochondria, and summarize mitomiRs that have been shown to play an important role in mitochondrial function, especially in the initiation and progression of breast cancer.
Collapse
Affiliation(s)
- Elif Erturk
- Bursa Uludag University, Vocational School of Health Services, 16059, Bursa, Turkey
| | - Omer Enes Onur
- Bursa Uludag University, Department of Biology, Science and Art Faculty, 16059, Bursa, Turkey
| | - Oguzhan Akgun
- Bursa Uludag University, Department of Biology, Science and Art Faculty, 16059, Bursa, Turkey
| | - Gonca Tuna
- Bursa Uludag University, Department of Biology, Science and Art Faculty, 16059, Bursa, Turkey
| | - Yaren Yildiz
- Bursa Uludag University, Department of Biology, Science and Art Faculty, 16059, Bursa, Turkey
| | - Ferda Ari
- Bursa Uludag University, Department of Biology, Science and Art Faculty, 16059, Bursa, Turkey.
| |
Collapse
|
45
|
Fan X, Yan T, Hou T, Xiong X, Feng L, Li S, Wang Z. Mitochondrial changes in fish cells in vitro in response to serum deprivation. FISH PHYSIOLOGY AND BIOCHEMISTRY 2022; 48:869-881. [PMID: 35652993 DOI: 10.1007/s10695-022-01088-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
Mitochondria are critical to cellular activity that implicated in expansive networks to maintain organismal homeostasis under external stimuli of nutrient variability, a common and severe stress to fish performance during the intensive culture conditions. In the present study, zebrafish embryonic fibroblast cells were used to investigate the fish mitochondrial changes upon serum deprivation. Results showed that mitochondrial content and membrane potential were significantly reduced with increased intracellular ROS level in the serum deprivation treated fish cells. And the impaired mitochondria were characterized by rough and fracted outer membrane, and more fused mitochondria were frequently observed with the upregulated mRNA expressions of mitochondrial fusion genes (mfn1b, mfn2, and opa1). Besides, the mitochondrial DNA (mtDNA) copy numbers of mtatp6, mtcox1, mtcytb, mtnd4, and mtnd6 were overall showing the highly significant reduction, together with the mRNA expressions of these genes significantly increased, exhibiting the compensatory effects in mitochondria. Furthermore, the methyl-cytosine of whole mtDNA was compared and the methyl-reads numbers were distinctly increased in the treatment group, reflecting the instability of fish mtDNA with mitochondrial dysfunction under nutrient fluctuations. Collectively, current findings could facilitate the integrated research between fish mitochondrial response and external variables that indicates the potentially profound and durative deficits in fish health during the aquaculture processes.
Collapse
Affiliation(s)
- Xiaoteng Fan
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Tao Yan
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Tingting Hou
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Xiaofan Xiong
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Leilei Feng
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Shiyi Li
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China
| | - Zaizhao Wang
- College of Animal Science and Technology, Northwest A&F University, 22 Xinong Road, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
46
|
Chen K, Lu P, Beeraka NM, Sukocheva OA, Madhunapantula SV, Liu J, Sinelnikov MY, Nikolenko VN, Bulygin KV, Mikhaleva LM, Reshetov IV, Gu Y, Zhang J, Cao Y, Somasundaram SG, Kirkland CE, Fan R, Aliev G. Mitochondrial mutations and mitoepigenetics: Focus on regulation of oxidative stress-induced responses in breast cancers. Semin Cancer Biol 2022; 83:556-569. [PMID: 33035656 DOI: 10.1016/j.semcancer.2020.09.012] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 02/08/2023]
Abstract
Epigenetic regulation of mitochondrial DNA (mtDNA) is an emerging and fast-developing field of research. Compared to regulation of nucler DNA, mechanisms of mtDNA epigenetic regulation (mitoepigenetics) remain less investigated. However, mitochondrial signaling directs various vital intracellular processes including aerobic respiration, apoptosis, cell proliferation and survival, nucleic acid synthesis, and oxidative stress. The later process and associated mismanagement of reactive oxygen species (ROS) cascade were associated with cancer progression. It has been demonstrated that cancer cells contain ROS/oxidative stress-mediated defects in mtDNA repair system and mitochondrial nucleoid protection. Furthermore, mtDNA is vulnerable to damage caused by somatic mutations, resulting in the dysfunction of the mitochondrial respiratory chain and energy production, which fosters further generation of ROS and promotes oncogenicity. Mitochondrial proteins are encoded by the collective mitochondrial genome that comprises both nuclear and mitochondrial genomes coupled by crosstalk. Recent reports determined the defects in the collective mitochondrial genome that are conducive to breast cancer initiation and progression. Mutational damage to mtDNA, as well as its overproliferation and deletions, were reported to alter the nuclear epigenetic landscape. Unbalanced mitoepigenetics and adverse regulation of oxidative phosphorylation (OXPHOS) can efficiently facilitate cancer cell survival. Accordingly, several mitochondria-targeting therapeutic agents (biguanides, OXPHOS inhibitors, vitamin-E analogues, and antibiotic bedaquiline) were suggested for future clinical trials in breast cancer patients. However, crosstalk mechanisms between altered mitoepigenetics and cancer-associated mtDNA mutations remain largely unclear. Hence, mtDNA mutations and epigenetic modifications could be considered as potential molecular markers for early diagnosis and targeted therapy of breast cancer. This review discusses the role of mitoepigenetic regulation in cancer cells and potential employment of mtDNA modifications as novel anti-cancer targets.
Collapse
Affiliation(s)
- Kuo Chen
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China; Institue for Regenerative Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Pengwei Lu
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China
| | - Narasimha M Beeraka
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka, India
| | - Olga A Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - SubbaRao V Madhunapantula
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka, India
| | - Junqi Liu
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Str., Zhengzhou, 450052, China
| | - Mikhail Y Sinelnikov
- Institue for Regenerative Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Vladimir N Nikolenko
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Department of Normal and Topographic Anatomy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University (MSU), 31-5 Lomonosovsky Prospect, 117192, Moscow, Russia
| | - Kirill V Bulygin
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Department of Normal and Topographic Anatomy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University (MSU), 31-5 Lomonosovsky Prospect, 117192, Moscow, Russia
| | - Liudmila M Mikhaleva
- Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russian Federation
| | - Igor V Reshetov
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Yuanting Gu
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China
| | - Jin Zhang
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Yu Cao
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Siva G Somasundaram
- Department of Biological Sciences, Salem University, 223 West Main Street Salem, WV, 26426, USA
| | - Cecil E Kirkland
- Department of Biological Sciences, Salem University, 223 West Main Street Salem, WV, 26426, USA
| | - Ruitai Fan
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China.
| | - Gjumrakch Aliev
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russian Federation; Institute of Physiologically Active Compounds of Russian Academy of Sciences, Severny pr. 1, Chernogolovka, Moscow Region, 142432, Russia; GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX, 78229, USA
| |
Collapse
|
47
|
Cammarata G, Barraco N, Giusti I, Gristina V, Dolo V, Taverna S. Extracellular Vesicles-ceRNAs as Ovarian Cancer Biomarkers: Looking into circRNA-miRNA-mRNA Code. Cancers (Basel) 2022; 14:cancers14143404. [PMID: 35884464 PMCID: PMC9324482 DOI: 10.3390/cancers14143404] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/09/2022] [Accepted: 07/12/2022] [Indexed: 02/08/2023] Open
Abstract
Simple Summary Patients with ovarian cancer have a very poor chance of long-term survival, usually due to advanced disease at the time of diagnosis. Emerging evidence suggests that extracellular vesicles contain noncoding RNAs such as microRNAs, piwiRNAs, circular RNAs, and long noncoding RNAs, with regulatory effects on ovarian cancer. In this review, we focus on ovarian cancer-associated circular RNA shuttled by extracellular vesicles as mediators of cancer progression and novel biomarkers in liquid biopsy. We propose a circular-RNA–microRNA-mRNA code that can reveal the regulatory network created by extracellular vesicles, noncoding RNAs, and mRNAs in ovarian cancer. Future research in this field will help to identify novel diagnostic biomarkers and druggable therapeutic targets, which will ultimately benefit patients. Abstract Ovarian cancer (OC) is one of the most lethal gynecologic malignancies in females worldwide. OC is frequently diagnosed at an advanced stage due to a lack of specific symptoms and effective screening tests, resulting in a poor prognosis for patients. Age, genetic alterations, and family history are the major risk factors for OC pathogenesis. Understanding the molecular mechanisms underlying OC progression, identifying new biomarkers for early detection, and discovering potential targets for new drugs are urgent needs. Liquid biopsy (LB), used for cancer detection and management, consists of a minimally invasive approach and practical alternative source to investigate tumor alterations by testing extracellular vesicles (EVs), circulating tumor cells, tumor-educated platelets, and cell-free nucleic acids. EVs are nanosize vesicles shuttling proteins, lipids, and nucleic acids, such as DNA, RNA, and non-coding RNAs (ncRNAs), that can induce phenotypic reprogramming of target cells. EVs are natural intercellular shuttles for ncRNAs, such as microRNAs (miRNAs) and circular-RNAs (circRNAs), known to have regulatory effects in OC. Here we focus on the involvement of circRNAs and miRNAs in OC cancer progression. The circRNA-microRNA-mRNA axis has been investigated with Circbank and miRwalk analysis, unraveling the intricate and detailed regulatory network created by EVs, ncRNAs, and mRNAs in OC.
Collapse
Affiliation(s)
- Giuseppe Cammarata
- Institute of Translational Pharmacology (IFT), National Research Council of Italy (CNR), 90146 Palermo, Italy
- Correspondence: (G.C.); (S.T.)
| | - Nadia Barraco
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy; (N.B.); (V.G.)
| | - Ilaria Giusti
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (I.G.); (V.D.)
| | - Valerio Gristina
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, 90127 Palermo, Italy; (N.B.); (V.G.)
| | - Vincenza Dolo
- Department of Life, Health and Environmental Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (I.G.); (V.D.)
| | - Simona Taverna
- Institute of Translational Pharmacology (IFT), National Research Council of Italy (CNR), 90146 Palermo, Italy
- Correspondence: (G.C.); (S.T.)
| |
Collapse
|
48
|
Moshareva MA, Lukyanov KA, Putlyaeva LV. Fluorescence imaging of epigenetic genome modifications. Biochem Biophys Res Commun 2022; 622:86-92. [PMID: 35843098 DOI: 10.1016/j.bbrc.2022.07.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Abstract
Epigenome contains a lot of information about cell state. Epigenetic analysis includes primarily sequence-based methods, which provide detailed data on distribution of modifications along the genome, but are poorly applicable for screenings. Specific fluorescence labeling and imaging of epigenetic modifications is an attractive complementary approach. It is currently based mainly on histone modifications study. We expect that inclusion of DNA modifications into imaging-based study would empower the method. In this review we discuss methods for fluorescence imaging of DNA modifications (mainly 5-methylcytosine). It opens an easy way to single cell analysis and high-throughput screening. Moreover, tracking epigenome changes in live cells becomes possible with genetically encoded probes.
Collapse
Affiliation(s)
- Maria A Moshareva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
| | - Konstantin A Lukyanov
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Lidia V Putlyaeva
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia.
| |
Collapse
|
49
|
Ziemann M, Wu W, Deng XL, Du XJ. Transcriptomic Analysis of Dysregulated Genes of the nDNA-mtDNA Axis in a Mouse Model of Dilated Cardiomyopathy. Front Genet 2022; 13:921610. [PMID: 35754828 PMCID: PMC9214240 DOI: 10.3389/fgene.2022.921610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 05/17/2022] [Indexed: 11/30/2022] Open
Abstract
Background: Mitochondrial dysfunction is implicated in the development of cardiomyopathy and heart failure. Transcription of mitochondrial DNA (mtDNA) encoded genes and subsequent protein synthesis are tightly regulated by nuclear DNA (nDNA) encoded proteins forming the nDNA-mtDNA axis. The scale of abnormalities in this axis in dilated cardiomyopathy (DCM) is unclear. We previously demonstrated, in a mouse DCM model with cardiac Mst1 overexpression, extensive downregulation of mitochondrial genes and mitochondrial dysfunction. Using the pre-acquired transcriptome sequencing database, we studied expression of gene sets of the nDNA-mtDNA axis. Methods: Using RNA-sequencing data from DCM hearts of mice at early and severe disease stages, transcriptome was performed for dysregulated nDNA-encoded gene sets that govern mtDNA transcription and in situ protein synthesis. To validate gene data, expression of a panel of proteins was determined by immunoblotting. Results: Relative to littermate controls, DCM hearts showed significant downregulation of all mtDNA encoded mRNAs, as well as mtDNA transcriptional activators. Downregulation was also evident for gene sets of mt-rRNA processing, aminoacyl-tRNA synthases, and mitoribosome subunits for in situ protein synthesis. Multiple downregulated genes belong to mitochondrial protein-importing machinery indicating compromised importing of proteins for mtDNA transcription and translation. Diverse changes were genes of mtRNA-binding proteins that govern maturation and stability of mtDNA-derived RNAs. Expression of mtDNA replicome genes was largely unchanged. These changes were similarly observed in mouse hearts at early and severe stages of DCM. Conclusion: Transcriptome revealed in our DCM model dysregulation of multiple gene sets of the nDNA-mtDNA axis, that is, expected to interfere with mtDNA transcription and in situ protein synthesis. Dysfunction of the nDNA-mtDNA axis might contribute to mitochondrial dysfunction and ultimately development of DCM.
Collapse
Affiliation(s)
- Mark Ziemann
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, Australia
| | - Wei Wu
- Key Laboratory of Environment and Genes Related to Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ministry of Education, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiu-Ling Deng
- Key Laboratory of Environment and Genes Related to Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ministry of Education, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Xiao-Jun Du
- Key Laboratory of Environment and Genes Related to Diseases, Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Ministry of Education, Xi'an Jiaotong University Health Science Center, Xi'an, China.,Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| |
Collapse
|
50
|
Luo S, Yang M, Zhao H, Han Y, Liu Y, Xiong X, Chen W, Li C, Sun L. Mitochondrial DNA-dependent inflammation in kidney diseases. Int Immunopharmacol 2022; 107:108637. [DOI: 10.1016/j.intimp.2022.108637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/11/2022] [Accepted: 02/15/2022] [Indexed: 11/15/2022]
|