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Srivastava LK, Ehrlicher AJ. Sensing the squeeze: nuclear mechanotransduction in health and disease. Nucleus 2024; 15:2374854. [PMID: 38951951 PMCID: PMC11221475 DOI: 10.1080/19491034.2024.2374854] [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: 02/23/2024] [Accepted: 06/26/2024] [Indexed: 07/03/2024] Open
Abstract
The nucleus not only is a repository for DNA but also a center of cellular and nuclear mechanotransduction. From nuclear deformation to the interplay between mechanosensing components and genetic control, the nucleus is poised at the nexus of mechanical forces and cellular function. Understanding the stresses acting on the nucleus, its mechanical properties, and their effects on gene expression is therefore crucial to appreciate its mechanosensitive function. In this review, we examine many elements of nuclear mechanotransduction, and discuss the repercussions on the health of cells and states of illness. By describing the processes that underlie nuclear mechanosensation and analyzing its effects on gene regulation, the review endeavors to open new avenues for studying nuclear mechanics in physiology and diseases.
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Affiliation(s)
| | - Allen J. Ehrlicher
- Department of Bioengineering, McGill University, Montreal, Canada
- Department of Biomedical Engineering, McGill University, Montreal, Canada
- Department of Anatomy and Cell Biology, McGill University, Montreal, Canada
- Centre for Structural Biology, McGill University, Montreal, Canada
- Department of Mechanical Engineering, McGill University, Montreal, Canada
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Canada
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2
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Yuan J, Yu Y, Li S, Zhang X, Zhang C, Li R, Hu J, Si S, Zhang C, Xiang J, Li F. Shrimp shapes a resistance trait against vibriosis by memorizing the colonization resistance of intestinal microbiota. PLoS Pathog 2024; 20:e1012321. [PMID: 38990823 PMCID: PMC11239079 DOI: 10.1371/journal.ppat.1012321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 06/06/2024] [Indexed: 07/13/2024] Open
Abstract
Vibriosis is one of the most serious diseases that commonly occurs in aquatic animals, thus, shaping a steady inherited resistance trait in organisms has received the highest priority in aquaculture. Whereas, the mechanisms underlying the development of such a resistance trait are mostly elusive. In this study, we constructed vibriosis-resistant and susceptible families of the Pacific white shrimp Litopenaeus vannamei after four generations of artificial selection. Microbiome sequencing indicated that shrimp can successfully develop a colonization resistance trait against Vibrio infections. This trait was characterized by a microbial community structure with specific enrichment of a single probiotic species (namely Shewanella algae), and notably, its formation was inheritable and might be memorized by host epigenetic remodeling. Regardless of the infection status, a group of genes was specifically activated in the resistant family through disruption of complete methylation. Specifically, hypo-methylation and hyper-expression of genes related to lactate dehydrogenase (LDH) and iron homeostasis might provide rich sources of specific carbon (lactate) and ions for the colonization of S. algae, which directly results in the reduction of Vibrio load in shrimp. Lactate feeding increased the survival of shrimp, while knockdown of LDH gene decreased the survival when shrimp was infected by Vibrio pathogens. In addition, treatment of shrimp with the methyltransferase inhibitor 5-azacytidine resulted in upregulations of LDH and some protein processing genes, significant enrichment of S. algae, and simultaneous reduction of Vibrio in shrimp. Our results suggest that the colonization resistance can be memorized as epigenetic information by the host, which has played a pivotal role in vibriosis resistance. The findings of this study will aid in disease control and the selection of superior lines of shrimp with high disease resistance.
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Affiliation(s)
- Jianbo Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
| | - Yang Yu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
| | - Shihao Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
| | - Xiaojun Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
| | - Chuntao Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Roujing Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Jie Hu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Shuqing Si
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Chengyi Zhang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jianhai Xiang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
| | - Fuhua Li
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega-Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture, Chinese Academy of Sciences, Wuhan, China
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Kim S, Han DJ, Lee SY, Moon Y, Kang SJ, Kim TM. A Subset of Microsatellite Unstable Cancer Genomes Prone to Short Insertions over Deletions Is Associated with Elevated Anticancer Immunity. Genes (Basel) 2024; 15:770. [PMID: 38927706 PMCID: PMC11202581 DOI: 10.3390/genes15060770] [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: 05/16/2024] [Revised: 06/10/2024] [Accepted: 06/10/2024] [Indexed: 06/28/2024] Open
Abstract
Deficiencies in DNA mismatch repair (MMRd) leave characteristic footprints of microsatellite instability (MSI) in cancer genomes. We used data from the Cancer Genome Atlas and International Cancer Genome Consortium to conduct a comprehensive analysis of MSI-associated cancers, focusing on indel mutational signatures. We classified MSI-high genomes into two subtypes based on their indel profiles: deletion-dominant (MMRd-del) and insertion-dominant (MMRd-ins). Compared with MMRd-del genomes, MMRd-ins genomes exhibit distinct mutational and transcriptomic features, including a higher prevalence of T>C substitutions and related mutation signatures. Short insertions and deletions in MMRd-ins and MMRd-del genomes target different sets of genes, resulting in distinct indel profiles between the two subtypes. In addition, indels in the MMRd-ins genomes are enriched with subclonal alterations that provide clues about a distinct evolutionary relationship between the MMRd-ins and MMRd-del genomes. Notably, the transcriptome analysis indicated that MMRd-ins cancers upregulate immune-related genes, show a high level of immune cell infiltration, and display an elevated neoantigen burden. The genomic and transcriptomic distinctions between the two types of MMRd genomes highlight the heterogeneity of genetic mechanisms and resulting genomic footprints and transcriptomic changes in cancers, which has potential clinical implications.
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Affiliation(s)
- Sunmin Kim
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Dong-Jin Han
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Seo-Young Lee
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Youngbeen Moon
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Su Jung Kang
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
| | - Tae-Min Kim
- Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea; (S.K.)
- Cancer Research Institute, College of Medicine, The Catholic University of Korea, Seoul 06591, Republic of Korea
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Republic of Korea
- CMC Institute for Basic Medical Science, The Catholic Medical Center, The Catholic University of Korea, Seoul 06591, Republic of Korea
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Ohi K, Fujikane D, Takai K, Kuramitsu A, Muto Y, Sugiyama S, Shioiri T. Epigenetic signatures of social anxiety, panic disorders and stress experiences: Insights from genome-wide DNA methylation risk scores. Psychiatry Res 2024; 337:115984. [PMID: 38820651 DOI: 10.1016/j.psychres.2024.115984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/15/2024] [Accepted: 05/26/2024] [Indexed: 06/02/2024]
Abstract
Social anxiety disorder (SAD) and panic disorder (PD) are prevalent anxiety disorders characterized by a complex interplay of genetic and environmental factors. Both disorders share overlapping features and often coexist, despite displaying distinct characteristics. Childhood life adversity, overall stressful life events, and genetic factors contribute to the development of these disorders. DNA methylation, an epigenetic modification, has been implicated in the pathogenesis of these diseases. In this study, we investigated whether whole-genome DNA methylation risk scores (MRSs) for SAD risk, severity of social anxiety, childhood life adversity, PD risk, and overall stressful life events were associated with SAD or PD case‒control status. Preliminary epigenome-wide association studies (EWASs) for SAD risk, severity of social anxiety, and childhood life adversity were conducted in 66 SAD individuals and 77 healthy controls (HCs). Similarly, EWASs for PD risk and overall stressful life events were performed in 182 PD individuals and 81 HCs. MRSs were calculated from these EWASs. MRSs derived from the EWASs of SAD risk and severity of social anxiety were greater in PD patients than in HCs. Additionally, MRSs derived from the EWASs of overall stressful life events, particularly in PD individuals, were lower in SAD individuals than in HCs. In contrast, MRSs for childhood life adversity or PD risk were not significantly associated with PD or SAD case‒control status. These findings highlight the epigenetic features shared in both disorders and the distinctive epigenetic features related to social avoidance in SAD patients, helping to elucidate the epigenetic basis of these disorders.
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Affiliation(s)
- Kazutaka Ohi
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan; Department of General Internal Medicine, Kanazawa Medical University, Ishikawa, Japan.
| | - Daisuke Fujikane
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Kentaro Takai
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Ayumi Kuramitsu
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Yukimasa Muto
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Shunsuke Sugiyama
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Toshiki Shioiri
- Department of Psychiatry, Gifu University Graduate School of Medicine, Gifu, Japan
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Labarga A, Martínez-Gonzalez J, Barajas M. Integrative Multi-Omics Analysis for Etiology Classification and Biomarker Discovery in Stroke: Advancing towards Precision Medicine. BIOLOGY 2024; 13:338. [PMID: 38785820 PMCID: PMC11149453 DOI: 10.3390/biology13050338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2024] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024]
Abstract
Recent advancements in high-throughput omics technologies have opened new avenues for investigating stroke at the molecular level and elucidating the intricate interactions among various molecular components. We present a novel approach for multi-omics data integration on knowledge graphs and have applied it to a stroke etiology classification task of 30 stroke patients through the integrative analysis of DNA methylation and mRNA, miRNA, and circRNA. This approach has demonstrated promising performance as compared to other existing single technology approaches.
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Affiliation(s)
- Alberto Labarga
- Health Science Department, Public University of Navarra, 31006 Pamplona, Spain;
| | | | - Miguel Barajas
- Health Science Department, Public University of Navarra, 31006 Pamplona, Spain;
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Islam M, Behura SK. Molecular Regulation of Fetal Brain Development in Inbred and Congenic Mouse Strains Differing in Longevity. Genes (Basel) 2024; 15:604. [PMID: 38790233 PMCID: PMC11121069 DOI: 10.3390/genes15050604] [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: 04/19/2024] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
The objective of this study was to investigate gene regulation of the developing fetal brain from congenic or inbred mice strains that differed in longevity. Gene expression and alternative splice variants were analyzed in a genome-wide manner in the fetal brain of C57BL/6J mice (long-lived) in comparison to B6.Cg-Cav1tm1Mls/J (congenic, short-lived) and AKR/J (inbred, short-lived) mice on day(d) 12, 15, and 17 of gestation. The analysis showed a contrasting gene expression pattern during fetal brain development in these mice. Genes related to brain development, aging, and the regulation of alternative splicing were significantly differentially regulated in the fetal brain of the short-lived compared to long-lived mice during development from d15 and d17. A significantly reduced number of splice variants was observed on d15 compared to d12 or d17 in a strain-dependent manner. An epigenetic clock analysis of d15 fetal brain identified DNA methylations that were significantly associated with single-nucleotide polymorphic sites between AKR/J and C57BL/6J strains. These methylations were associated with genes that show epigenetic changes in an age-correlated manner in mice. Together, the finding of this study suggest that fetal brain development and longevity are epigenetically linked, supporting the emerging concept of the early-life origin of longevity.
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Affiliation(s)
- Maliha Islam
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Susanta K. Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
- MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Reproduction and Health Group, University of Missouri, Columbia, MO 65211, USA
- Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO 65211, USA
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Abnizova I, Stapel C, Boekhorst RT, Lee JTH, Hemberg M. Integrative analysis of transcriptomic and epigenomic data reveals distinct patterns for developmental and housekeeping gene regulation. BMC Biol 2024; 22:78. [PMID: 38600550 PMCID: PMC11005181 DOI: 10.1186/s12915-024-01869-2] [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: 08/23/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Regulation of transcription is central to the emergence of new cell types during development, and it often involves activation of genes via proximal and distal regulatory regions. The activity of regulatory elements is determined by transcription factors (TFs) and epigenetic marks, but despite extensive mapping of such patterns, the extraction of regulatory principles remains challenging. RESULTS Here we study differentially and similarly expressed genes along with their associated epigenomic profiles, chromatin accessibility and DNA methylation, during lineage specification at gastrulation in mice. Comparison of the three lineages allows us to identify genomic and epigenomic features that distinguish the two classes of genes. We show that differentially expressed genes are primarily regulated by distal elements, while similarly expressed genes are controlled by proximal housekeeping regulatory programs. Differentially expressed genes are relatively isolated within topologically associated domains, while similarly expressed genes tend to be located in gene clusters. Transcription of differentially expressed genes is associated with differentially open chromatin at distal elements including enhancers, while that of similarly expressed genes is associated with ubiquitously accessible chromatin at promoters. CONCLUSION Based on these associations of (linearly) distal genes' transcription start sites (TSSs) and putative enhancers for developmental genes, our findings allow us to link putative enhancers to their target promoters and to infer lineage-specific repertoires of putative driver transcription factors, within which we define subgroups of pioneers and co-operators.
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Affiliation(s)
- Irina Abnizova
- Epigenetics Programme, Babraham Institute, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Carine Stapel
- Epigenetics Programme, Babraham Institute, Cambridge, UK
| | | | | | - Martin Hemberg
- Wellcome Sanger Institute, Hinxton, UK.
- The Gene Lay Institute of Immunology and Inflammation Brigham & Women's Hospital and Harvard Medical School, Boston, USA.
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Grondin A, Natividad MA, Ogata T, Jan A, Gaudin ACM, Trijatmiko KR, Liwanag E, Maruyama K, Fujita Y, Yamaguchi-Shinozaki K, Nakashima K, Slamet-Loedin IH, Henry A. A Case Study from the Overexpression of OsTZF5, Encoding a CCCH Tandem Zinc Finger Protein, in Rice Plants Across Nineteen Yield Trials. RICE (NEW YORK, N.Y.) 2024; 17:25. [PMID: 38592643 PMCID: PMC11003944 DOI: 10.1186/s12284-024-00705-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 03/29/2024] [Indexed: 04/10/2024]
Abstract
BACKGROUND Development of transgenic rice overexpressing transcription factors involved in drought response has been previously reported to confer drought tolerance and therefore represents a means of crop improvement. We transformed lowland rice IR64 with OsTZF5, encoding a CCCH-tandem zinc finger protein, under the control of the rice LIP9 stress-inducible promoter and compared the drought response of transgenic lines and nulls to IR64 in successive screenhouse paddy and field trials up to the T6 generation. RESULTS Compared to the well-watered conditions, the level of drought stress across experiments varied from a minimum of - 25 to - 75 kPa at a soil depth of 30 cm which reduced biomass by 30-55% and grain yield by 1-92%, presenting a range of drought severities. OsTZF5 transgenic lines showed high yield advantage under drought over IR64 in early generations, which was related to shorter time to flowering, lower shoot biomass and higher harvest index. However, the increases in values for yield and related traits in the transgenics became smaller over successive generations despite continued detection of drought-induced transgene expression as conferred by the LIP9 promoter. The decreased advantage of the transgenics over generations tended to coincide with increased levels of homozygosity. Background cleaning of the transgenic lines as well as introgression of the transgene into an IR64 line containing major-effect drought yield QTLs, which were evaluated starting at the BC3F1 and BC2F3 generation, respectively, did not result in consistently increased yield under drought as compared to the respective checks. CONCLUSIONS Although we cannot conclusively explain the genetic factors behind the loss of yield advantage of the transgenics under drought across generations, our results help in distinguishing among potential drought tolerance mechanisms related to effectiveness of the transgenics, since early flowering and harvest index most closely reflected the levels of yield advantage in the transgenics across generations while reduced biomass did not.
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Affiliation(s)
- Alexandre Grondin
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
- Institut de Recherche Pour Le Développement, Université de Montpellier, UMR DIADE, 911 Avenue Agropolis, 34394, Montpellier, France
| | - Mignon A Natividad
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
| | - Takuya Ogata
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Asad Jan
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
- Institute of Biotechnology and Genetics Engineering, The University of Agriculture, Peshawar, 25130, Khyber Pakhtunkhwa, Pakistan
| | - Amélie C M Gaudin
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
- Department of Plant Sciences, University of California Davis, Davis, CA, 95616, USA
| | - Kurniawan R Trijatmiko
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
| | - Evelyn Liwanag
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
| | - Kyonoshin Maruyama
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Yasunari Fujita
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Kazuko Yamaguchi-Shinozaki
- Biological Resources and Post-Harvest Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
- Laboratory of Plant Molecular Physiology, The University of Tokyo, Tokyo, 113-8657, Japan
- Tokyo University of Agriculture, Research Institute for Agricultural and Life Sciences, Tokyo, Japan
| | - Kazuo Nakashima
- Food Program, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, 305-8686, Japan
| | - Inez H Slamet-Loedin
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines
| | - Amelia Henry
- Rice Breeding Innovations Department, International Rice Research Institute, Pili Drive, Los Baños, Laguna, Philippines.
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Slowly M, Domingo-Relloso A, Santella RM, Haack K, Fallin DM, Terry MB, Rhoades DA, Herreros-Martinez M, Garcia-Esquinas E, Cole SA, Tellez-Plaza M, Navas-Acien A, Wu HC. Blood DNA methylation and liver cancer in American Indians: evidence from the Strong Heart Study. Cancer Causes Control 2024; 35:661-669. [PMID: 38010586 PMCID: PMC10960679 DOI: 10.1007/s10552-023-01822-8] [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: 04/29/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
PURPOSE Liver cancer incidence among American Indians/Alaska Natives has risen over the past 20 years. Peripheral blood DNA methylation may be associated with liver cancer and could be used as a biomarker for cancer risk. We evaluated the association of blood DNA methylation with risk of liver cancer. METHODS We conducted a prospective cohort study in 2324 American Indians, between age 45 and 75 years, from Arizona, Oklahoma, North Dakota and South Dakota who participated in the Strong Heart Study between 1989 and 1991. Liver cancer deaths (n = 21) were ascertained using death certificates obtained through 2017. The mean follow-up duration (SD) for non-cases was 25.1 (5.6) years and for cases, 11.0 (8.8) years. DNA methylation was assessed from blood samples collected at baseline using MethylationEPIC BeadChip 850 K arrays. We used Cox regression models adjusted for age, sex, center, body mass index, low-density lipoprotein cholesterol, smoking, alcohol consumption, and immune cell proportions to examine the associations. RESULTS We identified 9 CpG sites associated with liver cancer. cg16057201 annotated to MRFAP1) was hypermethylated among cases vs. non-cases (hazard ratio (HR) for one standard deviation increase in methylation was 1.25 (95% CI 1.14, 1.37). The other eight CpGs were hypomethylated and the corresponding HRs (95% CI) ranged from 0.58 (0.44, 0.75) for cg04967787 (annotated to PPRC1) to 0.77 (0.67, 0.88) for cg08550308. We also assessed 7 differentially methylated CpG sites associated with liver cancer in previous studies. The adjusted HR for cg15079934 (annotated to LPS1) was 1.93 (95% CI 1.10, 3.39). CONCLUSIONS Blood DNA methylation may be associated with liver cancer mortality and may be altered during the development of liver cancer.
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Affiliation(s)
- Monique Slowly
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Arce Domingo-Relloso
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
- Department of Statistics and Operations Research, University of Valencia, Valencia, Spain
| | - Regina M Santella
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Daniele M Fallin
- Department of Mental Health, Johns Hopkins University, Baltimore, MD, USA
- Department of Epidemiology, Johns Hopkins University, Baltimore, MD, USA
| | - Mary Beth Terry
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Dorothy A Rhoades
- Department of Medicine, Stephenson Cancer Center, University of Oklahoma Health Sciences, Oklahoma City, OK, USA
| | | | - Esther Garcia-Esquinas
- Universidad Autónoma de Madrid, Madrid, Spain
- CIBERESP (CIBER of Epidemiology and Public Health), Madrid, Spain
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA
| | - Hui-Chen Wu
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA.
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10
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Dirven BCJ, van Melis L, Daneva T, Dillen L, Homberg JR, Kozicz T, Henckens MJAG. Hippocampal Trauma Memory Processing Conveying Susceptibility to Traumatic Stress. Neuroscience 2024; 540:87-102. [PMID: 38220126 DOI: 10.1016/j.neuroscience.2024.01.007] [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: 02/27/2023] [Revised: 12/04/2023] [Accepted: 01/10/2024] [Indexed: 01/16/2024]
Abstract
While the majority of the population is ever exposed to a traumatic event during their lifetime, only a fraction develops posttraumatic stress disorder (PTSD). Disrupted trauma memory processing has been proposed as a core factor underlying PTSD symptomatology. We used transgenic Targeted-Recombination-in-Active-Populations (TRAP) mice to investigate potential alterations in trauma-related hippocampal memory engrams associated with the development of PTSD-like symptomatology. Mice were exposed to a stress-enhanced fear learning paradigm, in which prior exposure to a stressor affects the learning of a subsequent fearful event (contextual fear conditioning using foot shocks), during which neuronal activity was labeled. One week later, mice were behaviorally phenotyped to identify mice resilient and susceptible to developing PTSD-like symptomatology. Three weeks post-learning, mice were re-exposed to the conditioning context to induce remote fear memory recall, and associated hippocampal neuronal activity was assessed. While no differences in the size of the hippocampal neuronal ensemble activated during fear learning were observed between groups, susceptible mice displayed a smaller ensemble activated upon remote fear memory recall in the ventral CA1, higher regional hippocampal parvalbuminneuronal density and a relatively lower activity of parvalbumininterneurons upon recall. Investigation of potential epigenetic regulators of the engram revealed rather generic (rather than engram-specific) differences between groups, with susceptible mice displaying lower hippocampal histone deacetylase 2 expression, and higher methylation and hydroxymethylation levels. These finding implicate variation in epigenetic regulation within the hippocampus, as well as reduced regional hippocampal activity during remote fear memory recall in interindividual differences in susceptibility to traumatic stress.
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Affiliation(s)
- Bart C J Dirven
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands; Department of Medical Imaging, Anatomy, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Lennart van Melis
- Department of Medical Imaging, Anatomy, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Teya Daneva
- Department of Medical Imaging, Anatomy, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Lieke Dillen
- Department of Medical Imaging, Anatomy, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Judith R Homberg
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands
| | - Tamas Kozicz
- Department of Medical Imaging, Anatomy, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands; Center for Individualized Medicine, Department of Clinical Genomics, and Biochemical Genetics Laboratory, Mayo Clinic, Rochester, MN 55905, USA; University of Pecs Medical School, Department of Anatomy, Pecs, Hungary
| | - Marloes J A G Henckens
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behaviour, Radboud University Medical Centre, 6500 HB Nijmegen, The Netherlands.
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11
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Delphin N, Aust C, Griffiths L, Fernandez F. Epigenetic Regulation in Schizophrenia: Focus on Methylation and Histone Modifications in Human Studies. Genes (Basel) 2024; 15:272. [PMID: 38540331 PMCID: PMC10970389 DOI: 10.3390/genes15030272] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 02/17/2024] [Accepted: 02/19/2024] [Indexed: 06/15/2024] Open
Abstract
Despite extensive research over the last few decades, the etiology of schizophrenia (SZ) remains unclear. SZ is a pathological disorder that is highly debilitating and deeply affects the lifestyle and minds of those affected. Several factors (one or in combination) have been reported as contributors to SZ pathogenesis, including neurodevelopmental, environmental, genetic and epigenetic factors. Deoxyribonucleic acid (DNA) methylation and post-translational modification (PTM) of histone proteins are potentially contributing epigenetic processes involved in transcriptional activity, chromatin folding, cell division and apoptotic processes, and DNA damage and repair. After establishing a summary of epigenetic processes in the context of schizophrenia, this review aims to highlight the current understanding of the role of DNA methylation and histone PTMs in this disorder and their potential roles in schizophrenia pathophysiology and pathogenesis.
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Affiliation(s)
- Natasha Delphin
- School of Health and Behavioural Sciences, Faculty of Health Sciences, Australian Catholic University, 1100 Nudgee Rd, Banyo, QLD 4014, Australia; (N.D.)
| | - Caitlin Aust
- School of Health and Behavioural Sciences, Faculty of Health Sciences, Australian Catholic University, 1100 Nudgee Rd, Banyo, QLD 4014, Australia; (N.D.)
| | - Lyn Griffiths
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia;
| | - Francesca Fernandez
- School of Health and Behavioural Sciences, Faculty of Health Sciences, Australian Catholic University, 1100 Nudgee Rd, Banyo, QLD 4014, Australia; (N.D.)
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, 60 Musk Ave, Kelvin Grove, QLD 4059, Australia;
- Healthy Brain and Mind Research Centre, Australian Catholic University, Melbourne, VIC 3000, Australia
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12
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Bou Ghanem A, Hussayni Y, Kadbey R, Ratel Y, Yehya S, Khouzami L, Ghadieh HE, Kanaan A, Azar S, Harb F. Exploring the complexities of 1C metabolism: implications in aging and neurodegenerative diseases. Front Aging Neurosci 2024; 15:1322419. [PMID: 38239489 PMCID: PMC10794399 DOI: 10.3389/fnagi.2023.1322419] [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: 10/16/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
The intricate interplay of one-carbon metabolism (OCM) with various cellular processes has garnered substantial attention due to its fundamental implications in several biological processes. OCM serves as a pivotal hub for methyl group donation in vital biochemical reactions, influencing DNA methylation, protein synthesis, and redox balance. In the context of aging, OCM dysregulation can contribute to epigenetic modifications and aberrant redox states, accentuating cellular senescence and age-associated pathologies. Furthermore, OCM's intricate involvement in cancer progression is evident through its capacity to provide essential one-carbon units crucial for nucleotide synthesis and DNA methylation, thereby fueling uncontrolled cell proliferation and tumor development. In neurodegenerative disorders like Alzheimer's and Parkinson's, perturbations in OCM pathways are implicated in the dysregulation of neurotransmitter synthesis and mitochondrial dysfunction, contributing to disease pathophysiology. This review underscores the profound impact of OCM in diverse disease contexts, reinforcing the need for a comprehensive understanding of its molecular complexities to pave the way for targeted therapeutic interventions across inflammation, aging and neurodegenerative disorders.
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Affiliation(s)
- Ayman Bou Ghanem
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Yaman Hussayni
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Raghid Kadbey
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Yara Ratel
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Shereen Yehya
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Lara Khouzami
- College of Natural and Health Sciences, Zayed University, Dubai, United Arab Emirates
| | - Hilda E. Ghadieh
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
- AUB Diabetes, American University of Beirut Medical Center, Beirut, Lebanon
| | - Amjad Kanaan
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Sami Azar
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
| | - Frederic Harb
- Faculty of Medicine and Medical Sciences, University of Balamand, Tripoli, Lebanon
- AUB Diabetes, American University of Beirut Medical Center, Beirut, Lebanon
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13
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Zhou BW, Wu QQ, Mauki DH, Wang X, Zhang SR, Yin TT, Chen FL, Li C, Liu YH, Wang GD, Zhang YP. Germline gene fusions across species reveal the chromosomal instability regions and cancer susceptibility. iScience 2023; 26:108431. [PMID: 38205119 PMCID: PMC10777377 DOI: 10.1016/j.isci.2023.108431] [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: 02/01/2023] [Revised: 06/24/2023] [Accepted: 11/08/2023] [Indexed: 01/12/2024] Open
Abstract
The canine transmissible venereal tumor (CTVT) is a clonal cell-mediated cancer with a long evolutionary history and extensive karyotype rearrangements in its genome. However, little is known about its genetic similarity to human tumors. Here, using multi-omics data we identified 11 germline gene fusions (GGFs) in CTVT, which showed higher genetic susceptibility than others. Additionally, we illustrate a mechanism of a complex gene fusion of three gene segments (HSD17B4-DMXL1-TNFAIP8) that we refer to "greedy fusion". Our findings also provided evidence that expressions of GGFs are downregulated during the tumor regressive phase, which is associated with DNA methylation level. This study presents a comprehensive landscape of gene fusions (GFs) in CTVT, which offers a valuable genetic resource for exploring potential genetic mechanisms underlying the development of cancers in both dogs and humans.
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Affiliation(s)
- Bo-Wen Zhou
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Qing-Qin Wu
- School of Ecology and Environmental Sciences, Yunnan University, Kunming, Yunnan 650500, China
| | - David H. Mauki
- Institute of Neurological Disease, National-Local Joint Engineering Research Center of Translational Medicine, State Key Lab of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xuan Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Shu-Run Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Ting-Ting Yin
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Fang-Liang Chen
- Kunming Police Dog Base of the Ministry of Public Security, Kunming, Yunnan 650204, China
| | - Chao Li
- State Key Laboratory for Conservation and Utilization of Bio-Resource, Yunnan University, Kunming, Yunnan 650500, China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution & Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
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14
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Strawn M, Safranski TJ, Behura SK. Does DNA methylation in the fetal brain leave an epigenetic memory in the blood? Gene 2023; 887:147788. [PMID: 37696423 DOI: 10.1016/j.gene.2023.147788] [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: 07/11/2023] [Revised: 08/23/2023] [Accepted: 09/07/2023] [Indexed: 09/13/2023]
Abstract
Epigenetic memory is an emerging concept that refers to the process in which epigenetic changes occurring early-in life can lead to long-term programs of gene regulation in time and space. By leveraging neural network regression modeling of DNA methylation data in pigs, we show that specific methylations in the adult blood can reliably predict methylation changes that occurred in the fetal brain. Genes associated with these methylations represented known markers of specific cell types of blood including bone marrow hematopoietic progenitor cells, and ependymal and oligodendrocyte cells of brain. This suggested that methylation changes that occurred in the developing brain were maintained as an epigenetic memory in the blood through the adult life.
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Affiliation(s)
- Monica Strawn
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Timothy J Safranski
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, United States; MU Institute for Data Science and Informatics, University of Missouri, Columbia, MO 65211, United States; Interdisciplinary Neuroscience Program, University of Missouri, Columbia, MO 65211, United States.
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15
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Xia L, Wu T, Chen L, Mei P, Liu L, Li R, Shu M, Huan Z, Wu C, Fang B. Silicon-Based Biomaterials Modulate the Adaptive Immune Response of T Lymphocytes to Promote Osteogenesis/Angiogenesis via Epigenetic Regulation. Adv Healthc Mater 2023; 12:e2302054. [PMID: 37842937 DOI: 10.1002/adhm.202302054] [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: 06/30/2023] [Revised: 10/11/2023] [Indexed: 10/17/2023]
Abstract
Silicon (Si)-based biomaterials are widely applied for bone regeneration. However, the underlying mechanisms of the materials function remain largely unknown. T lymphocyte-mediated adaptive immune response plays a vital role in the process of bone regeneration. In the current study, mesoporous silica (MS) is used as a model material of Si-based biomaterials. It shows that the supernatant of CD4+ T lymphocytes pretreated with MS extract significantly promotes the vascularized bone regeneration. The potential mechanism is closely related to the fact that MS extract can reduce the expression of regulatory factor X-1 (RFX-1) in CD4+ T lymphocytes. This may result in the overexpression of interleukin-17A (IL-17A) by boosting histone H3 acetylation and lowering DNA methylation and H3K9 trimethylation. Importantly, the in vivo experiments further reveal that MS particles significantly enhance bone regeneration with improved angiogenesis in the critical-sized calvarial defect mouse model accompanied by upregulation of IL-17A in peripheral blood and the proportion of Th17 cells. This study suggests that modulation of the adaptive immune response of T lymphocytes by silicate-based biomaterials plays an important role for bone regeneration.
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Affiliation(s)
- Lunguo Xia
- Department of Orthodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Tingting Wu
- Department of Orthodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, 200011, China
- College & Hospital of Stomatology, Anhui Medical University, Key Laboratory of Oral Diseases Research of Anhui Province, Hefei, 230032, China
| | - Lei Chen
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, 200050, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Mei
- Department of Orthodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Lu Liu
- Department of Orthodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Ruomei Li
- Department of Orthodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Mengmeng Shu
- Department of Orthodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, 200011, China
| | - Zhiguang Huan
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, 200050, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengtie Wu
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai, 200050, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bing Fang
- Department of Orthodontics, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, National Clinical Research Center for Oral Diseases, Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, Shanghai, 200011, China
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16
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Zhu L, Sun L, Liu W, Han W, Huang G, Li J. Long-term storage does not affect the DNA methylation profiles of vitrified-warmed human embryos. Mol Reprod Dev 2023. [PMID: 37882215 DOI: 10.1002/mrd.23713] [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: 05/29/2023] [Revised: 08/31/2023] [Accepted: 09/24/2023] [Indexed: 10/27/2023]
Abstract
With the widespread application of embryo cryopreservation in assisted reproductive techniques, it is necessary to assess the safety of long-term cryopreservation of human embryos and it is unclear whether storage time has an impact on the DNA methylation profiles of human embryos. Nine women who received IVF treatment were recruited for this study. The retrieved eight-cell human embryos were classified into three groups including fresh embryos, cryopreserved embryos stored for 3 years, and cryopreserved embryos stored for 8 years. Single-cell whole-genome bisulfite sequencing (scWGBS) was conducted. The genome-wide methylation pattern of the fresh and two cryopreserved groups were similar. In addition, the methylation level in different genomic regions showed comparable patterns and no significant differences were observed in the methylation level of imprinted genes among the three groups. A total of 587 differentially methylated regions (DMRs) in the 3-year group and 540 DMRs in the 8-year group were identified comparing to fresh group. However, they were not enriched in promoters and had a similar genome-wide distributions, suggesting that these DMRs may not contribute to the changes in corresponding gene expressions. Our study illustrated that long-term cryopreservation will not affect the DNA methylation profiles of human eight-cell embryos at single-cell level.
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Affiliation(s)
- Ling Zhu
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Liwei Sun
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Weiwei Liu
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Wei Han
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Guoning Huang
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
| | - Jingyu Li
- Chongqing Key Laboratory of Human Embryo Engineering, Center for Reproductive Medicine, Women and Children's Hospital of Chongqing Medical University, Chongqing, China
- Chongqing Clinical Research Center for Reproductive Medicine, Chongqing Health Center for Women and Children, Chongqing, China
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17
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Cao G, Jia H, Xu S, Xu E, Wang P, Xue Q, Wang H. Tetrahedral DNA nanostructure-corbelled click chemistry-based large-scale assembly of nanozymes for ratiometric fluorescence assay of DNA methyltransferase activity. J Mater Chem B 2023; 11:9912-9921. [PMID: 37850305 DOI: 10.1039/d3tb01795h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Ligation efficiency in a surface-based DNA click chemistry (CuAAC) reaction is extremely restricted by the orientation and density of probes arranged on a heterogeneous surface. Herein, we engineer DNA tetrahedral nanostructure (DTN)-corbelled click chemistry to trigger a hybridization chain reaction (HCR) assembling a large-scale of nanozymes for ratiometric fluorescence detection of DNA adenine methyltransferase (Dam). In this study, a DNA tetrahedron structure with an alkynyl modifying pendant DNA probe (Alk-DTN) is designed and assembled on a magnetic bead (MB) as a scaffold for click chemistry. When a CuO NP-encoded magnetic nanoparticle (CuO-MNP) substrate was methylated by Dam, CuO NPs were released and turned into a mass of Cu+. The Cu+ droves azido modifying lDNA (azide-lDNA) to connect with the Alk-DTN probe on the MB through the click reaction, forming an intact primer to initiate the HCR. The HCR product, a rigid structure double-stranded DNA, periodically assembles glucose oxidase mimicking gold nanoparticles (GNPs) into a large-scale of nanozymes for catalyzing the oxidation of glucose to H2O2. NH2-MIL-101 MOFs, a fluorescent indicator and a biomimetic catalyst, activated the product H2O2 to oxidize o-phenylenediamine (oPD) into visually detectable 2,3-diaminophenazine (DAP). The change of the signal ratio between DAP and NH2-MIL-101 is proportional to the methylation event corresponding to the MTase activity. In this study, the DTN enhances the efficiency of the surface-based DNA click reaction and maintains the catalytic activities of gold nanoparticle nanozymes due to the intrinsic nature of mechanical rigidity and well-controlled orientation and well-adjusted size. Large-scale assembly of nanozymes circumvents the loss of natural enzyme activity caused by chemical modification and greatly improves the amplification efficiency. The proposed biosensor displayed a low detection limit of 0.001 U mL-1 for Dam MTase due to multiple amplification and was effective in real samples and methylation inhibitor screening, providing a promising modular platform for bioanalysis.
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Affiliation(s)
- Guohui Cao
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Huiying Jia
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Shuling Xu
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Ensheng Xu
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Pin Wang
- Neurology of Department, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, P. R. China.
| | - Qingwang Xue
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China.
| | - Huaisheng Wang
- School of Chemistry and Chemical Engineering, Liaocheng University, Liaocheng, 252059, Shandong, China.
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18
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Camilo V, Pacheco MB, Moreira-Silva F, Outeiro-Pinho G, Gaspar VM, Mano JF, Marques CJ, Henrique R, Jerónimo C. Novel Insights on the Role of Epigenetics in Androgen Receptor's Expression in Prostate Cancer. Biomolecules 2023; 13:1526. [PMID: 37892208 PMCID: PMC10605369 DOI: 10.3390/biom13101526] [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: 08/28/2023] [Revised: 10/04/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
The androgens/androgen receptor (AR) axis is the main therapeutic target in prostate cancer (PCa). However, while initially responsive, a subset of tumors loses AR expression through mechanisms putatively associated with epigenetic modifications. In this study, we assessed the link between the presence of CpG methylation in the 5'UTR and promoter regions of AR and loss of AR expression. Hence, we characterized and compared the methylation signature at CpG resolution of these regulatory regions in vitro, both at basal levels and following treatment with 5-aza-2-deoxycytidine (DAC) alone, or in combination with Trichostatin A (TSA). Our results showed heterogeneity in the methylation signature of AR negative cell lines and pinpointed the proximal promoter region as the most consistently methylated site in DU-145. Furthermore, this region was extremely resistant to the demethylating effects of DAC and was only significantly demethylated upon concomitant treatment with TSA. Nevertheless, no AR re-expression was detected at the mRNA or protein level. Importantly, after treatment, there was a significant increase in repressive histone marks at AR region 1 in DU-145 cells. Altogether, our data indicate that AR region 1 genomic availability is crucial for AR expression and that the inhibition of histone methyltransferases might hold promise for AR re-expression.
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Affiliation(s)
- Vânia Camilo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
| | - Mariana Brütt Pacheco
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
| | - Filipa Moreira-Silva
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
| | - Gonçalo Outeiro-Pinho
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
| | - Vítor M. Gaspar
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (V.M.G.)
| | - João F. Mano
- CICECO—Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal; (V.M.G.)
| | - C. Joana Marques
- Genetics Unit, Department of Pathology, Faculty of Medicine, University of Porto (FMUP), Alameda Prof. Hernâni Monteiro, 4200-319 Porto, Portugal;
- i3S-Institute for Research and Innovation in Health, University of Porto, R. Alfredo Allen 208, 4200-135 Porto, Portugal
| | - Rui Henrique
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto), Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Biology and Epigenetics Group, Research Center of IPO Porto (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center (Porto.CCC) Raquel Seruca, R. Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal; (V.C.); (M.B.P.); (F.M.-S.); (G.O.-P.); (R.H.)
- Department of Pathology and Molecular Immunology, ICBAS-School of Medicine and Biomedical Sciences, University of Porto, Rua Jorge Viterbo Ferreira nº 228, 4050-313 Porto, Portugal
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19
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Cao TV, Sutherland HG, Benton MC, Haupt LM, Lea RA, Griffiths LR. Exploring the Functional Basis of Epigenetic Aging in Relation to Body Fat Phenotypes in the Norfolk Island Cohort. Curr Issues Mol Biol 2023; 45:7862-7877. [PMID: 37886940 PMCID: PMC10605526 DOI: 10.3390/cimb45100497] [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: 08/15/2023] [Revised: 09/18/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
DNA methylation is an epigenetic factor that is modifiable and can change over a lifespan. While many studies have identified methylation sites (CpGs) related to aging, the relationship of these to gene function and age-related disease phenotypes remains unclear. This research explores this question by testing for the conjoint association of age-related CpGs with gene expression and the relation of these to body fat phenotypes. The study included blood-based gene transcripts and intragenic CpG methylation data from Illumina 450 K arrays in 74 healthy adults from the Norfolk Island population. First, a series of regression analyses were performed to detect associations between gene transcript level and intragenic CpGs and their conjoint relationship with age. Second, we explored how these age-related expression CpGs (eCpGs) correlated with obesity-related phenotypes, including body fat percentage, body mass index, and waist-to-hip ratio. We identified 35 age-related eCpGs associated with age. Of these, ten eCpGs were associated with at least one body fat phenotype. Collagen Type XI Alpha 2 Chain (COL11A2), Complement C1s (C1s), and four and a half LIM domains 2 (FHL2) genes were among the most significant genes with multiple eCpGs associated with both age and multiple body fat phenotypes. The COL11A2 gene contributes to the correct assembly of the extracellular matrix in maintaining the healthy structural arrangement of various components, with the C1s gene part of complement systems functioning in inflammation. Moreover, FHL2 expression was upregulated under hypermethylation in both blood and adipose tissue with aging. These results suggest new targets for future studies and require further validation to confirm the specific function of these genes on body fat regulation.
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Affiliation(s)
- Thao Van Cao
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
| | - Heidi G. Sutherland
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
| | - Miles C. Benton
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
| | - Larisa M. Haupt
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
- ARC Training Centre for Cell and Tissue Engineering Technologies, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia
- Max Planck Queensland Centre for the Materials Sciences of Extracellular Matrices, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia
| | - Rodney A. Lea
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
| | - Lyn R. Griffiths
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology (QUT), Kelvin Grove, QLD 4059, Australia; (T.V.C.); (H.G.S.); (M.C.B.); (L.M.H.); (L.R.G.)
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20
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Zuberi A, Huang Y, Dotts AJ, Wei H, Coon JS, Liu S, Iizuka T, Wu O, Sotos O, Saini P, Chakravarti D, Boyer TG, Dai Y, Bulun SE, Yin P. MED12 mutation activates the tryptophan/kynurenine/AHR pathway to promote growth of uterine leiomyomas. JCI Insight 2023; 8:e171305. [PMID: 37607000 PMCID: PMC10561729 DOI: 10.1172/jci.insight.171305] [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: 04/13/2023] [Accepted: 08/15/2023] [Indexed: 08/23/2023] Open
Abstract
Uterine leiomyomas cause heavy menstrual bleeding, anemia, and pregnancy loss in millions of women worldwide. Driver mutations in the transcriptional mediator complex subunit 12 (MED12) gene in uterine myometrial cells initiate 70% of leiomyomas that grow in a progesterone-dependent manner. We showed a distinct chromatin occupancy landscape of MED12 in mutant MED12 (mut-MED12) versus WT-MED12 leiomyomas. Integration of cistromic and transcriptomics data identified tryptophan 2,3-dioxygenase (TDO2) as the top mut-MED12 target gene that was significantly upregulated in mut-MED12 leiomyomas when compared with adjacent myometrium and WT-MED12 leiomyomas. TDO2 catalyzes the conversion of tryptophan to kynurenine, an aryl hydrocarbon receptor (AHR) ligand that we confirmed to be significantly elevated in mut-MED12 leiomyomas. Treatment of primary mut-MED12 leiomyoma cells with tryptophan or kynurenine stimulated AHR nuclear translocation, increased proliferation, inhibited apoptosis, and induced AHR-target gene expression, whereas blocking the TDO2/kynurenine/AHR pathway by siRNA or pharmacological treatment abolished these effects. Progesterone receptors regulated the expression of AHR and its target genes. In vivo, TDO2 expression positively correlated with the expression of genes crucial for leiomyoma growth. In summary, activation of the TDO2/kynurenine/AHR pathway selectively in mut-MED12 leiomyomas promoted tumor growth and may inform the future development of targeted treatments and precision medicine.
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Affiliation(s)
- Azna Zuberi
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Yongchao Huang
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ariel J. Dotts
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Helen Wei
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - John S. Coon
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Shimeng Liu
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Takashi Iizuka
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Olivia Wu
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Olivia Sotos
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Priyanka Saini
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Debabrata Chakravarti
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Thomas G. Boyer
- Department of Molecular Medicine, Institute of Biotechnology, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Yang Dai
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Serdar E. Bulun
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Ping Yin
- Division of Reproductive Science in Medicine, Department of Obstetrics & Gynecology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
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21
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Eichenauer H, Ehlert U. The association between prenatal famine, DNA methylation and mental disorders: a systematic review and meta-analysis. Clin Epigenetics 2023; 15:152. [PMID: 37716973 PMCID: PMC10505322 DOI: 10.1186/s13148-023-01557-y] [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: 05/02/2023] [Accepted: 08/14/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND Undernutrition in pregnant women is an unfavorable environmental condition that can affect the intrauterine development via epigenetic mechanisms and thus have long-lasting detrimental consequences for the mental health of the offspring later in life. One epigenetic mechanism that has been associated with mental disorders and undernutrition is alterations in DNA methylation. The effect of prenatal undernutrition on the mental health of adult offspring can be analyzed through quasi-experimental studies such as famine studies. The present systematic review and meta-analysis aims to analyze the association between prenatal famine exposure, DNA methylation, and mental disorders in adult offspring. We further investigate whether altered DNA methylation as a result of prenatal famine exposure is prospectively linked to mental disorders. METHODS We conducted a systematic search of the databases PubMed and PsycINFO to identify relevant records up to September 2022 on offspring whose mothers experienced famine directly before and/or during pregnancy, examining the impact of prenatal famine exposure on the offspring's DNA methylation and/or mental disorders or symptoms. RESULTS The systematic review showed that adults who were prenatally exposed to famine had an increased risk of schizophrenia and depression. Several studies reported an association between prenatal famine exposure and hyper- or hypomethylation of specific genes. The largest number of studies reported differences in DNA methylation of the IGF2 gene. Altered DNA methylation of the DUSP22 gene mediated the association between prenatal famine exposure and schizophrenia in adult offspring. Meta-analysis confirmed the increased risk of schizophrenia following prenatal famine exposure. For DNA methylation, meta-analysis was not suitable due to different microarrays/data processing approaches and/or unavailable data. CONCLUSION Prenatal famine exposure is associated with an increased risk of mental disorders and DNA methylation changes. The findings suggest that changes in DNA methylation of genes involved in neuronal, neuroendocrine, and immune processes may be a mechanism that promotes the development of mental disorders such as schizophrenia and depression in adult offspring. Such findings are crucial given that undernutrition has risen worldwide, increasing the risk of famine and thus also of negative effects on mental health.
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Affiliation(s)
- Heike Eichenauer
- Clinical Psychology and Psychotherapy, University of Zurich, Binzmühlestrasse 14, 8050, Zurich, Switzerland
| | - Ulrike Ehlert
- Clinical Psychology and Psychotherapy, University of Zurich, Binzmühlestrasse 14, 8050, Zurich, Switzerland.
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22
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Bar-Sadeh B, Pnueli L, Keestra S, Bentley GR, Melamed P. Srd5a1 is Differentially Regulated and Methylated During Prepubertal Development in the Ovary and Hypothalamus. J Endocr Soc 2023; 7:bvad108. [PMID: 37646011 PMCID: PMC10461783 DOI: 10.1210/jendso/bvad108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Indexed: 09/01/2023] Open
Abstract
5α-reductase-1 catalyzes production of various steroids, including neurosteroids. We reported previously that expression of its encoding gene, Srd5a1, drops in murine ovaries and hypothalamic preoptic area (POA) after early-life immune stress, seemingly contributing to delayed puberty and ovarian follicle depletion, and in the ovaries the first intron was more methylated at two CpGs. Here, we hypothesized that this CpG-containing locus comprises a methylation-sensitive transcriptional enhancer for Srd5a1. We found that ovarian Srd5a1 mRNA increased 8-fold and methylation of the same two CpGs decreased up to 75% between postnatal days 10 and 30. Estradiol (E2) levels rise during this prepubertal stage, and exposure of ovarian cells to E2 increased Srd5a1 expression. Chromatin immunoprecipitation in an ovarian cell line confirmed ESR1 binding to this differentially methylated genomic region and enrichment of the enhancer modification, H3K4me1. Targeting dCas9-DNMT3 to this locus increased CpG2 methylation 2.5-fold and abolished the Srd5a1 response to E2. In the POA, Srd5a1 mRNA levels decreased 70% between postnatal days 7 and 10 and then remained constant without correlation to CpG methylation levels. Srd5a1 mRNA levels did not respond to E2 in hypothalamic GT1-7 cells, even after dCas9-TET1 reduced CpG1 methylation by 50%. The neonatal drop in POA Srd5a1 expression occurs at a time of increasing glucocorticoids, and treatment of GT1-7 cells with dexamethasone reduced Srd5a1 mRNA levels; chromatin immunoprecipitation confirmed glucocorticoid receptor binding at the enhancer. Our findings on the tissue-specific regulation of Srd5a1 and its methylation-sensitive control by E2 in the ovaries illuminate epigenetic mechanisms underlying reproductive phenotypic variation that impact life-long health.
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Affiliation(s)
- Ben Bar-Sadeh
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Lilach Pnueli
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Sarai Keestra
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
- Department of Anthropology, Durham University, Durham, DH1 3LE, UK
| | | | - Philippa Melamed
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 32000, Israel
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23
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Ju H, Bai J, Jiang J, Che Y, Chen X. Comparative evaluation and analysis of DNA N4-methylcytosine methylation sites using deep learning. Front Genet 2023; 14:1254827. [PMID: 37671040 PMCID: PMC10476523 DOI: 10.3389/fgene.2023.1254827] [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: 07/07/2023] [Accepted: 07/31/2023] [Indexed: 09/07/2023] Open
Abstract
DNA N4-methylcytosine (4mC) is significantly involved in biological processes, such as DNA expression, repair, and replication. Therefore, accurate prediction methods are urgently needed. Deep learning methods have transformed applications that previously require sequencing expertise into engineering challenges that do not require expertise to solve. Here, we compare a variety of state-of-the-art deep learning models on six benchmark datasets to evaluate their performance in 4mC methylation site detection. We visualize the statistical analysis of the datasets and the performance of different deep-learning models. We conclude that deep learning can greatly expand the potential of methylation site prediction.
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Affiliation(s)
- Hong Ju
- Heilongjiang Agricultural Engineering Vocational College, Harbin, China
| | - Jie Bai
- Engineering Research Center of Integration and Application of Digital Learning Technology, Ministry of Education, Hangzhou, China
| | - Jing Jiang
- Beidahuang Industry Group General Hospital, Harbin, China
| | - Yusheng Che
- Heilongjiang Agricultural Engineering Vocational College, Harbin, China
| | - Xin Chen
- Department of Neurosurgical Laboratory, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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24
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Flack N, Drown M, Walls C, Pratte J, McLain A, Faulk C. Chromosome-level, nanopore-only genome and allele-specific DNA methylation of Pallas's cat, Otocolobus manul. NAR Genom Bioinform 2023; 5:lqad033. [PMID: 37025970 PMCID: PMC10071556 DOI: 10.1093/nargab/lqad033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/10/2023] [Accepted: 03/17/2023] [Indexed: 04/07/2023] Open
Abstract
Pallas's cat, or the manul cat (Otocolobus manul), is a small felid native to the grasslands and steppes of central Asia. Population strongholds in Mongolia and China face growing challenges from climate change, habitat fragmentation, poaching, and other sources. These threats, combined with O. manul's zoo collection popularity and value in evolutionary biology, necessitate improvement of species genomic resources. We used standalone nanopore sequencing to assemble a 2.5 Gb, 61-contig nuclear assembly and 17097 bp mitogenome for O. manul. The primary nuclear assembly had 56× sequencing coverage, a contig N50 of 118 Mb, and a 94.7% BUSCO completeness score for Carnivora-specific genes. High genome collinearity within Felidae permitted alignment-based scaffolding onto the fishing cat (Prionailurus viverrinus) reference genome. Manul contigs spanned all 19 felid chromosomes with an inferred total gap length of less than 400 kilobases. Modified basecalling and variant phasing produced an alternate pseudohaplotype assembly and allele-specific DNA methylation calls; 61 differentially methylated regions were identified between haplotypes. Nearest features included classical imprinted genes, non-coding RNAs, and putative novel imprinted loci. The assembled mitogenome successfully resolved existing discordance between Felinae nuclear and mtDNA phylogenies. All assembly drafts were generated from 158 Gb of sequence using seven minION flow cells.
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Affiliation(s)
- Nicole Flack
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA
| | - Melissa Drown
- Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, MN 55108, USA
| | - Carrie Walls
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
| | - Jay Pratte
- Bloomington Parks and Recreation, Miller Park Zoo, Bloomington, IL 61701, USA
| | - Adam McLain
- Department of Biology and Chemistry, SUNY Polytechnic Institute, Utica, NY 13502, USA
| | - Christopher Faulk
- Department of Animal Science, University of Minnesota, Saint Paul, MN 55108, USA
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25
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Hua Y, Huang C, Guo Y, Du X, Guo L, Wang W, Lu C, Guo L. Association between academic pressure, NR3C1 gene methylation, and anxiety symptoms among Chinese adolescents: a nested case-control study. BMC Psychiatry 2023; 23:376. [PMID: 37254074 DOI: 10.1186/s12888-023-04816-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 04/24/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Academic pressure is a prevalent stressor among Chinese adolescents and is often linked to anxiety symptoms, although the underlying mechanism remains unclear. This study aimed to investigate the association between NR3C1 gene methylation, academic pressure, and anxiety symptoms among Chinese adolescents. METHODS This nested-case control study included 150 adolescents (boys: 38.7%; baseline age: 12-17 years) from a school-based longitudinal study of Chinese adolescents. Cases (n = 50) were defined as those with anxiety symptoms at both baseline and follow-up, while controls (n = 100) were randomly selected from those without anxiety symptoms at both timepoints. The cases and controls were 1:2 matched by age. Academic pressure, anxiety symptoms, and potential covariates were measured using a self-report questionnaire. Peripheral whole blood samples were collected from each participant for the detection of cortisol level (i.e., morning serum cortisol level) and DNA methylation. The methylation analysis included a total of 27 CpG units at the NR3C1 promoter region. RESULTS The final adjusted models showed that students with heavy academic pressure at baseline were at a higher risk of anxiety symptoms at follow-up compared to those with mild academic pressure (β estimate: 6.24 [95% CI: 3.48 ~ 9.01]). After adjusting for covariates, the methylation level of one CpG unit (NR3C1-16 CpG10) in NR3C1 differed significantly between cases and controls (F = 6.188, P = 0.014), and the difference remained significant after correction for multiple testing (P < 0.025). The adjusted regression models showed that moderate (β estimate = 0.010 [95% CI: 0.000 ~ 0.020], P = 0.046) and heavy (β estimate = 0.011 [95% CI: 0.001 ~ 0.020], P = 0.030) academic pressure were significantly associated with the methylation level of NR3C1-16 CpG 10. Further mediation analysis demonstrated that the association of academic pressure and anxiety symptoms was significantly mediated by the methylation of NR3C1-16 CpG 10 (β estimate for indirect effect = 0.11 [95% CI: 0.005 ~ 0.32]; indirect/total effect = 8.3%). CONCLUSION The present study suggests that NR3C1-16 CpG 10 DNA methylation might be a potential mechanism that partially explains the lasting effects of academic pressure on subsequent anxiety symptoms among adolescents. Further studies with larger sample sizes are recommended to replicate this finding.
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Affiliation(s)
- Yilin Hua
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, 74 Zhongshan Rd 2, 510080, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, 510080, Guangzhou, People's Republic of China
| | - Cuihong Huang
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, 74 Zhongshan Rd 2, 510080, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, 510080, Guangzhou, People's Republic of China
| | - Yangfeng Guo
- Health Promotion Center for Primary and Secondary Schools, Guangzhou, People's Republic of China
| | - Xueying Du
- Health Promotion Center for Primary and Secondary Schools, Guangzhou, People's Republic of China
| | - Liling Guo
- Health Promotion Center for Primary and Secondary Schools, Guangzhou, People's Republic of China
| | - Wanxin Wang
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, 74 Zhongshan Rd 2, 510080, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, 510080, Guangzhou, People's Republic of China
| | - Ciyong Lu
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, 74 Zhongshan Rd 2, 510080, Guangzhou, People's Republic of China
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, 510080, Guangzhou, People's Republic of China
| | - Lan Guo
- Department of Medical Statistics and Epidemiology, School of Public Health, Sun Yat-sen University, 74 Zhongshan Rd 2, 510080, Guangzhou, People's Republic of China.
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Sun Yat-sen University, 510080, Guangzhou, People's Republic of China.
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26
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Alameda L, Liu Z, Sham PC, Aas M, Trotta G, Rodriguez V, Di Forti M, Stilo SA, Kandaswamy R, Arango C, Arrojo M, Bernardo M, Bobes J, de Haan L, Del-Ben CM, Gayer-Anderson C, Sideli L, Jones PB, Jongsma HE, Kirkbride JB, La Cascia C, Lasalvia A, Tosato S, Llorca PM, Menezes PR, van Os J, Quattrone D, Rutten BP, Santos JL, Sanjuán J, Selten JP, Szöke A, Tarricone I, Tortelli A, Velthorst E, Morgan C, Dempster E, Hannon E, Burrage J, Dwir D, Arumuham A, Mill J, Murray RM, Wong CCY. Exploring the mediation of DNA methylation across the epigenome between childhood adversity and First Episode of Psychosis-findings from the EU-GEI study. Mol Psychiatry 2023; 28:2095-2106. [PMID: 37062770 DOI: 10.1038/s41380-023-02044-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/04/2023] [Accepted: 03/20/2023] [Indexed: 04/18/2023]
Abstract
ABTRACT Studies conducted in psychotic disorders have shown that DNA-methylation (DNAm) is sensitive to the impact of Childhood Adversity (CA). However, whether it mediates the association between CA and psychosis is yet to be explored. Epigenome wide association studies (EWAS) using the Illumina Infinium-Methylation EPIC array in peripheral blood tissue from 366 First-episode of psychosis and 517 healthy controls was performed. Adversity scores were created for abuse, neglect and composite adversity with the Childhood Trauma Questionnaire (CTQ). Regressions examining (I) CTQ scores with psychosis; (II) with DNAm EWAS level and (III) between DNAm and caseness, adjusted for a variety of confounders were conducted. Divide-Aggregate Composite-null Test for the composite null-hypothesis of no mediation effect was conducted. Enrichment analyses were conducted with missMethyl package and the KEGG database. Our results show that CA was associated with psychosis (Composite: OR = 1.68; p = <0.001; abuse: OR = 2.16; p < 0.001; neglect: OR = 2.27; p = <0.001). None of the CpG sites significantly mediated the adversity-psychosis association after Bonferroni correction (p < 8.1 × 10-8). However, 28, 34 and 29 differentially methylated probes associated with 21, 27, 20 genes passed a less stringent discovery threshold (p < 5 × 10-5) for composite, abuse and neglect respectively, with a lack of overlap between abuse and neglect. These included genes previously associated to psychosis in EWAS studies, such as PANK1, SPEG TBKBP1, TSNARE1 or H2R. Downstream gene ontology analyses did not reveal any biological pathways that survived false discovery rate correction. Although at a non-significant level, DNAm changes in genes previously associated with schizophrenia in EWAS studies may mediate the CA-psychosis association. These results and associated involved processes such as mitochondrial or histaminergic disfunction, immunity or neural signalling requires replication in well powered samples. The lack of overlap between mediating genes associated with abuse and neglect suggests differential biological trajectories linking CA subtypes and psychosis.
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Affiliation(s)
- Luis Alameda
- Service of General Psychiatry, Treatment and Early Intervention in Psychosis Program, Lausanne University Hospital (CHUV), Lausanne, Switzerland.
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK.
- Instituto de Investigación Sanitaria de Sevilla, IbiS, Hospital Universitario Virgen del Rocío, Department of Psychiatry, Universidad de Sevilla, Seville, Spain.
| | - Zhonghua Liu
- Department of Biostatistics, Columbia University, New York, NY, USA
| | - Pak C Sham
- Department of Psychiatry, State Key Laboratory of Brain and Cognitive Sciences, and Centre for PanorOmic Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Monica Aas
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Giulia Trotta
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Victoria Rodriguez
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
| | - Marta Di Forti
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Simona A Stilo
- Department of Mental Health and Addiction Services, ASP Crotone, Crotone, Italy
| | - Radhika Kandaswamy
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Celso Arango
- Department of Child and Adolescent Psychiatry, Institute of Psychiatry and Mental Health, Hospital General Universitario Gregorio Marañón, School of Medicine, Universidad Complutense, IiSGM, CIBERSAM, Madrid, Spain
| | - Manuel Arrojo
- Department of Psychiatry, Psychiatric Genetic Group, Instituto de Investigación Sanitaria de Santiago de Compostela, Complejo Hospitalario Universitario de Santiago de Compostela, Santiago, Spain
| | - Miguel Bernardo
- Barcelona Clinic Schizophrenia Unit, Neuroscience Institute, Hospital Clinic of Barcelona, University of Barcelona, Institut d'Investigacions Biomèdiques August Pi I Sunyer, Biomedical Research Networking Centre in Mental Health (CIBERSAM), Barcelona, Spain
| | - Julio Bobes
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Oviedo, Spain
- Department of Medicine, Psychiatry Area, School of Medicine, Universidad de Oviedo, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Oviedo, Spain
| | - Lieuwe de Haan
- Department of Psychiatry, Early Psychosis Section, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Cristina Marta Del-Ben
- Neuroscience and Behaviour Department, Ribeirão Preto Medical School, University of São Paulo, São Paulo, Brazil
| | | | - Lucia Sideli
- LUMSA University, Department of Human Science and Department of Psychosis Studies, KCL, Rome, Italy
| | - Peter B Jones
- Department of Psychiatry, University of Cambridge, Cambridge, UK
- CAMEO Early Intervention Service, Cambridgeshire & Peterborough NHS Foundation Trust, Cambridge, UK
| | - Hannah E Jongsma
- Psylife Group, Division of Psychiatry, University College London, London, UK
| | - James B Kirkbride
- Psylife Group, Division of Psychiatry, University College London, London, UK
| | - Caterina La Cascia
- Section of Psychiatry, Department of Biomedicine, Neuroscience and advanced Diagnostic (BiND), University of Palermo, Palermo, Italy
| | - Antonio Lasalvia
- Section of Psychiatry, Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | - Sarah Tosato
- Section of Psychiatry, Department of Neuroscience, Biomedicine and Movement, University of Verona, Verona, Italy
| | | | - Paulo Rossi Menezes
- Department of Preventive Medicine, Faculdade de Medicina, Universidade de São Paulo, São Paulo, Brazil
| | - Jim van Os
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, South Limburg Mental Health Research and Teaching Network, Maastricht University Medical Centre, Maastricht, The Netherlands
- Department Psychiatry, Brain Centre Rudolf Magnus, Utrecht University Medical Centre, Utrecht, The Netherlands
| | - Diego Quattrone
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Bart P Rutten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, South Limburg Mental Health Research and Teaching Network, Maastricht University Medical Centre, Maastricht, The Netherlands
| | - Jose Luis Santos
- Department of Psychiatry, Servicio de Psiquiatría Hos"ital "Virgen de"a Luz", C/Hermandad de Donantes de Sangre, 16002, Cuenca, Spain
| | - Julio Sanjuán
- Department of Psychiatry, School of Medicine, Universidad de Valencia, Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), C/Avda. Blasco Ibáñez 15, 46010, Valencia, Spain
| | - Jean-Paul Selten
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience, South Limburg Mental Health Research and Teaching Network, Maastricht University Medical Centre, Maastricht, The Netherlands
- Rivierduinen Institute for Mental Health Care, Leiden, The Netherlands
| | - Andrei Szöke
- University of Paris Est Creteil, INSERM, IMRB, AP-HP, Hôpitaux Universitaires, H. Mondor, DMU IMPACT, Creteil, France
| | - Ilaria Tarricone
- Bologna Transcultural Psychosomatic Team (BoTPT), Department of Medical and Surgical Science, Alma Mater Studiorum Università di Bologna, Bologna, Italy
| | | | - Eva Velthorst
- GGZ (Mental Health Services) Noord Holland Noord, Heerhugowaard, the Netherlands
| | - Craig Morgan
- ESRC Centre for Society and Mental Health, King's College London, London, UK
| | - Emma Dempster
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Eilis Hannon
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Joe Burrage
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Daniella Dwir
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Atheeshaan Arumuham
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
- Psychiatric Imaging Group, MRC London Institute of Medical Sciences, London, UK
- South London and Maudsley NHS Foundation Trust, London, UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, UK
| | - Jonathan Mill
- Department of Psychiatry, Center for Psychiatric Neuroscience, Lausanne University Hospital (CHUV), Lausanne, Switzerland
| | - Robin M Murray
- Psychosis Studies, Institute of Psychiatry, Psychology and Neuroscience. King's College of London, London, UK
| | - Chloe C Y Wong
- Social, Genetics and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
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Cheon H, Hur JK, Hwang W, Yang HJ, Son JH. Epigenetic modification of gene expression in cancer cells by terahertz demethylation. Sci Rep 2023; 13:4930. [PMID: 36967404 PMCID: PMC10040409 DOI: 10.1038/s41598-023-31828-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
Terahertz (THz) radiation can affect the degree of DNA methylation, the spectral characteristics of which exist in the terahertz region. DNA methylation is an epigenetic modification in which a methyl (CH3) group is attached to cytosine, a nucleobase in human DNA. Appropriately controlled DNA methylation leads to proper regulation of gene expression. However, abnormal gene expression that departs from controlled genetic transcription through aberrant DNA methylation may occur in cancer or other diseases. In this study, we demonstrate the modification of gene expression in cells by THz demethylation using resonant THz radiation. Using an enzyme-linked immunosorbent assay, we observed changes in the degree of global DNA methylation in the SK-MEL-3 melanoma cell line under irradiation with 1.6-THz radiation with limited spectral bandwidth. Resonant THz radiation demethylated living melanoma cells by 19%, with no significant occurrence of apurinic/apyrimidinic sites, and the demethylation ratio was linearly proportional to the power of THz radiation. THz demethylation downregulates FOS, JUN, and CXCL8 genes, which are involved in cancer and apoptosis pathways. Our results show that THz demethylation has the potential to be a gene expression modifier with promising applications in cancer treatment.
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Affiliation(s)
- Hwayeong Cheon
- Biomedical Engineering Research Center, Asan Medical Center, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, 05505, Republic of Korea
| | - Junho K Hur
- Department of Genetics, College of Medicine, Graduate School of Biomedical Sciences and Engineering, Hanyang University, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Woochang Hwang
- Department of Pre-Medicine, College of Medicine, Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Hee-Jin Yang
- Department of Neurosurgery, Seoul National University Boramae Medical Center, 20 Boramae-ro 5-gil, Dognjak-gu, Seoul, 07061, Republic of Korea.
| | - Joo-Hiuk Son
- Department of Physics, University of Seoul, 163, Seoulsiripdae-ro, Dongdaemun-gu, Seoul, 02504, Republic of Korea.
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28
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Fallet M, Blanc M, Di Criscio M, Antczak P, Engwall M, Guerrero Bosagna C, Rüegg J, Keiter SH. Present and future challenges for the investigation of transgenerational epigenetic inheritance. ENVIRONMENT INTERNATIONAL 2023; 172:107776. [PMID: 36731188 DOI: 10.1016/j.envint.2023.107776] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
Epigenetic pathways are essential in different biological processes and in phenotype-environment interactions in response to different stressors and they can induce phenotypic plasticity. They encompass several processes that are mitotically and, in some cases, meiotically heritable, so they can be transferred to subsequent generations via the germline. Transgenerational Epigenetic Inheritance (TEI) describes the phenomenon that phenotypic traits, such as changes in fertility, metabolic function, or behavior, induced by environmental factors (e.g., parental care, pathogens, pollutants, climate change), can be transferred to offspring generations via epigenetic mechanisms. Investigations on TEI contribute to deciphering the role of epigenetic mechanisms in adaptation, adversity, and evolution. However, molecular mechanisms underlying the transmission of epigenetic changes between generations, and the downstream chain of events leading to persistent phenotypic changes, remain unclear. Therefore, inter-, (transmission of information between parental and offspring generation via direct exposure) and transgenerational (transmission of information through several generations with disappearance of the triggering factor) consequences of epigenetic modifications remain major issues in the field of modern biology. In this article, we review and describe the major gaps and issues still encountered in the TEI field: the general challenges faced in epigenetic research; deciphering the key epigenetic mechanisms in inheritance processes; identifying the relevant drivers for TEI and implement a collaborative and multi-disciplinary approach to study TEI. Finally, we provide suggestions on how to overcome these challenges and ultimately be able to identify the specific contribution of epigenetics in transgenerational inheritance and use the correct tools for environmental science investigation and biomarkers identification.
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Affiliation(s)
- Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden; Department of Biochemistry, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd, Oxford OX1 3QU, United Kingdom.
| | - Mélanie Blanc
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, INRAE, Palavas, France
| | - Michela Di Criscio
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Philipp Antczak
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Center for Molecular Medicine Cologne, Germany; Excellence Cluster on Cellular Stress Responses in Aging Associated Diseases, University of Cologne, Cologne, Germany
| | - Magnus Engwall
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
| | | | - Joëlle Rüegg
- Department of Organismal Biology, Uppsala University, Norbyv. 18A, 75236 Uppsala, Sweden
| | - Steffen H Keiter
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182 Örebro, Sweden
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29
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Inserra A, Campanale A, Cheishvili D, Dymov S, Wong A, Marcal N, Syme RA, Taylor L, De Gregorio D, Kennedy TE, Szyf M, Gobbi G. Modulation of DNA methylation and protein expression in the prefrontal cortex by repeated administration of D-lysergic acid diethylamide (LSD): Impact on neurotropic, neurotrophic, and neuroplasticity signaling. Prog Neuropsychopharmacol Biol Psychiatry 2022; 119:110594. [PMID: 35777526 DOI: 10.1016/j.pnpbp.2022.110594] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 11/18/2022]
Abstract
AIM Psychedelic compounds elicit relief from mental disorders. However, the underpinnings of therapeutic improvement remain poorly understood. Here, we investigated the effects of repeated lysergic acid diethylamide (LSD) on whole-genome DNA methylation and protein expression in the mouse prefrontal cortex (PFC). METHODS Whole genome bisulphite sequencing (WGBS) and proteomics profiling of the mouse prefrontal cortex (PFC) were performed to assess DNA methylation and protein expression changes following 7 days of repeated LSD administration (30 μg/kg/day); a treatment we previously found to potentiate excitatory neurotransmission and to increase dendritic spine density in the PFC in mice. qRT-PCR was employed to validate candidate genes detected in both analyses. RESULTS LSD significantly modulated DNA methylation in 635 CpG sites of the mouse PFC, and in an independent cohort the expression level of 178 proteins. Gene signaling pathways affected are involved in nervous system development, axon guidance, synaptic plasticity, quantity and cell viability of neurons and protein translation. Four genes and their protein product were detected as differentially methylated and expressed, and their transcription was increased. Specifically, Coronin 7 (Coro7), an axon guidance cue; Penta-EF-Hand Domain Containing 1 (Pef1), an mTORC1 and cell cycle modulator; Ribosomal Protein S24 (Rps24), required for pre-rRNA maturation and biogenesis of proteins involved with cell proliferation and migration, and Abhydrolase Domain Containing 6, Acylglycerol Lipase (Abhd6), a post-synaptic lipase. CONCLUSIONS LSD affects DNA methylation, altering gene expression and protein expression related to neurotropic-, neurotrophic- and neuroplasticity signaling. This could represent a core mechanism mediating the effects of psychedelics.
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Affiliation(s)
- Antonio Inserra
- Neurobiological Psychiatry Unit, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Antonella Campanale
- Neurobiological Psychiatry Unit, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - David Cheishvili
- Department of Oncology, McGill University, Montreal, QC, Canada; HKG Epitherapeutics, Hong Kong
| | - Sergiy Dymov
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Amy Wong
- Proteomics Platform, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Nathalie Marcal
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | | | - Lorne Taylor
- Proteomics Platform, Research Institute of the McGill University Health Center, Montreal, QC, Canada
| | - Danilo De Gregorio
- Neurobiological Psychiatry Unit, Department of Psychiatry, McGill University, Montreal, QC, Canada
| | - Timothy E Kennedy
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Gabriella Gobbi
- Neurobiological Psychiatry Unit, Department of Psychiatry, McGill University, Montreal, QC, Canada.
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30
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Anand C, Maia PD, Torok J, Mezias C, Raj A. The effects of microglia on tauopathy progression can be quantified using Nexopathy in silico (Nexis) models. Sci Rep 2022; 12:21170. [PMID: 36477076 PMCID: PMC9729195 DOI: 10.1038/s41598-022-25131-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
Abstract
The prion-like transsynaptic propagation of misfolded tau along the brain's connectome has previously been modeled using connectome-based network diffusion models. In addition to the connectome, interactions between the general neurological "milieu" in the neurodegenerative brain and proteinopathic species can also contribute to pathology propagation. Such a molecular nexopathy framework posits that the distinct characteristics of neurodegenerative disorders stem from interactions between the network and surrounding molecular players. However, the effects of these modulators remain unquantified. Here, we present Nexopathy in silico ("Nexis"), a quantitative model of tau progression augmenting earlier models by including parameters of pathology propagation defined by the molecular modulators of connectome-based spread. Our Nexis:microglia model provides the first quantitative characterization of this effect on the whole brain by expanding previous models of neuropathology progression by incorporating microglial influence. We show that Trem2, but not microglial homeostasis genes, significantly improved the model's predictive power. Trem2 appears to reduce tau accumulation rate while increasing its interregional spread from the hippocampal seed area, causing higher tau burden in the striatum, pallidum, and contralateral hippocampus. Nexis provides an improved understanding and quantification of microglial contribution to tau propagation and can be flexibly modified to include other modulators of progressive neurodegeneration.
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Affiliation(s)
- Chaitali Anand
- grid.266102.10000 0001 2297 6811Department of Radiology, University of California San Francisco, San Francisco, CA USA
| | - Pedro D. Maia
- grid.267315.40000 0001 2181 9515Department of Mathematics, University of Texas at Arlington, Arlington, TX USA
| | - Justin Torok
- grid.266102.10000 0001 2297 6811Department of Radiology, University of California San Francisco, San Francisco, CA USA
| | - Christopher Mezias
- grid.225279.90000 0004 0387 3667Department of Neuroscience, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY USA
| | - Ashish Raj
- grid.266102.10000 0001 2297 6811Department of Radiology, University of California San Francisco, San Francisco, CA USA
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31
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Cai G, Yu X, Hutchins D, McDermott S. A pilot study that provides evidence of epigenetic changes among mother-child pairs living proximal to mining in the US. ENVIRONMENTAL GEOCHEMISTRY AND HEALTH 2022; 44:4735-4746. [PMID: 35137284 PMCID: PMC9468238 DOI: 10.1007/s10653-022-01217-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Environmental exposures to chemicals can disrupt gene expression, and the effects could be mediated by methylation. This investigation focused on methylation of genes associated with exposure to metals. Mother-child pairs from three locations in Montana were recruited, and buccal cells were collected for genome-wide methylation assay. Four pairs were from Butte, where there is mining and a Superfund site, four pairs were from Anaconda with a Superfund site, and four pairs were from Missoula with neither a mine nor a Superfund site. Principal component analysis, linear mixed models, hierarchical clustering and heatmap, and gene set enrichment analysis were used to visualize the profiles, identify the top associated methylation loci, and investigate the involved pathways. Distinctly higher or lower methylation in samples from Butte were found at the top differentially methylated loci. The 200 genes harboring the most hypermethylated loci were significantly enriched in genes involved in actin cytoskeleton regulation, ABC transporters, leukocyte transendothelial migration, focal adhesion, and adherens junction, which plays a role in pathogenesis of disease, including autism spectrum disorders. This study lays a foundation for inquiry about genetic changes associated with environmental exposure to metals for people living in proximity to Superfund and open pit mining.
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Affiliation(s)
- Guoshuai Cai
- Department of Environmental Health Sciences, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - Xuanxuan Yu
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
| | - David Hutchins
- Department of Epidemiology and Biostatistics, Arnold School of Public Health, University of South Carolina, Columbia, SC, USA
- Montana Technological University, Butte, MT, USA
| | - Suzanne McDermott
- Department of Environmental, Occupational, and Geospatial Health Sciences, CUNY Graduate School of Public Health & Health Policy, New York, NY, USA.
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32
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Sapozhnikov DM, Szyf M. Enzyme-free targeted DNA demethylation using CRISPR-dCas9-based steric hindrance to identify DNA methylation marks causal to altered gene expression. Nat Protoc 2022; 17:2840-2881. [PMID: 36207463 DOI: 10.1038/s41596-022-00741-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022]
Abstract
DNA methylation involves the enzymatic addition of a methyl group primarily to cytosine residues in DNA. This protocol describes how to produce complete and minimally confounded DNA demethylation of specific sites in the genome of cultured cells by clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9 and without the involvement of an epigenetic-modifying enzyme, the purpose of which is the evaluation of the functional (i.e., gene expression or phenotypic) consequences of DNA demethylation of specific sites that have been previously implicated in particular pathological or physiological contexts. This protocol maximizes the ability of the easily reprogrammable CRISPR-dCas9 system to assess the impact of DNA methylation from a causal rather than correlational perspective: alternative protocols for CRISPR-dCas9-based site-specific DNA methylation or demethylation rely on the recruitment of epigenetic enzymes that exhibit additional nonspecific activities at both the targeted site and throughout the genome, confounding conclusions of causality of DNA methylation. Inhibition or loss of DNA methylation is accomplished by three consecutive lentiviral transductions. The first two lentiviruses establish stable expression of dCas9 and a guide RNA, which will physically obstruct either maintenance or de novo DNA methyltransferase activity at the guide RNA target site. A third lentivirus introduces Cre recombinase to delete the dCas9 transgene, which leads to loss of dCas9 from the target site, allowing transcription factors and/or the transcription machinery to interact with the demethylated target site. This protocol requires 3-8 months to complete owing to prolonged cell passaging times, but there is little hands-on time, and no specific skills beyond basic molecular biology techniques are necessary.
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Affiliation(s)
- Daniel M Sapozhnikov
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada.
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33
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Lin S, Yi S, Qiu P. Comprehensive analysis of TCGA data reveals correlation between DNA methylation and alternative splicing. BMC Genomics 2022; 23:758. [PMID: 36401166 PMCID: PMC9675104 DOI: 10.1186/s12864-022-08992-w] [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: 04/11/2022] [Accepted: 11/05/2022] [Indexed: 11/21/2022] Open
Abstract
The effect of DNA methylation on the regulation of gene expression has been extensively discussed in the literature. However, the potential association between DNA methylation and alternative splicing is not understood well. In this study, we integrated multiple omics data types from The Cancer Genome Atlas (TCGA) and systematically examined the relationship between DNA methylation and alternative splicing. Using the methylation data and exon expression data, we identified many CpG sites significantly associated with exon expression in various types of cancers. We further observed that the direction and strength of significant CpG-exon correlation tended to be consistent across different cancer contexts, indicating that some CpG-exon correlation patterns reflect fundamental biological mechanisms that transcend tissue- and cancer- types. We also discovered that CpG sites correlated with exon expressions were more likely to be associated with patient survival outcomes compared to CpG sites that did not correlate with exon expressions. Furthermore, we found that CpG sites were more strongly correlated with exon expression than expression of isoforms harboring the corresponding exons. This observation suggests that a major effect of CpG methylation on alternative splicing may be related to the inclusion or exclusion of exons, which subsequently impacts the relative usage of various isoforms. Overall, our study revealed correlation patterns between DNA methylation and alternative splicing, which provides new insights into the role of methylation in the transcriptional process.
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Affiliation(s)
- Shuting Lin
- grid.213917.f0000 0001 2097 4943School of Biological Sciences, Georgia Institute of Technology, Atlanta, USA
| | - Soojin Yi
- grid.133342.40000 0004 1936 9676Ecology, Evolution, Marine Biology, University of California, Santa Barbara, Santa Barbara, USA
| | - Peng Qiu
- grid.213917.f0000 0001 2097 4943Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, USA
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34
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Ho CM, Yen TL, Chien TY, Huang SH. Distinct promotor methylation at tumor suppressive genes in ovarian cancer stromal progenitor cells and ovarian cancer and its clinical implication. Am J Cancer Res 2022; 12:5325-5341. [PMID: 36504889 PMCID: PMC9729910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/12/2022] [Indexed: 12/15/2022] Open
Abstract
Aberrant CpG-island methylation affects ovarian cancer progression. The promotor methylation changes at tumor suppressive genes in ovarian cancer stromal progenitor cells (OCSPCs) and epithelial ovarian cancer (EOC) tissues and their clinical implication remains unexplored. We systemically analyzed the promoter methylation status of 40 tumor suppressor genes (TSGs) associated with cancer in paired epithelial-like and mesenchymal-like OCSPCs and ovarian cancer cells by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA). The effect of DNA methylation on gene expression was confirmed using qRT-PCR. The differential frequencies of TSGs' promoter methylation among matched epithelial-like or mesenchymal-like OCSPCs from tissues and ascites and ovarian cancer tissues were further validated in cancer tissues and correlated with clinicopathological features and survival outcomes of patients. According to the promoter methylation frequencies of the 40 TSGs, promoters of RASSF1A were the only significantly hypomethylated in epithelial-like OCSPCs from tissues than those from ascites and bulk tumor cells (0% vs 38% vs 45%, P=0.039 by Fisher's exact test). The most frequencies at promotor hypermethylation of TSGs in mesenchymal-like OCSPCs from ascites which processed aggressiveness were CDKN2B (73%) followed by CCND2 (45%) and RASSF1A (45%). Forty-three percent (47/110) of RASSF1A and 45% of CCND2 were validated as a frequently hypermethylated gene in an independent set of 110 EOC tissues in contrast to none (0/60) and 12% (10/60) of benign ovarian cysts (both P<0.001). Functional experiments revealed overexpression of CCND2 or CDKN2B in MSc-OCSPCs decreases EMT, invasion, and spheroid formation in EOC, and abolishes DNMT1 and COL6A3 expression. However, for the expected 5-year overall survival (OS) for patients with methylated RASSF1A, CCND2, and CDKN2B, only RASSF1A was significantly worse than those without methylated RASSF1A (56% vs 80%, p=0.022). Taken together, overexpression of CCND2 and CDKN2B decreased the aggressiveness of mesenchymal-like OCSPCs from ascites which may represent a potential therapeutic target for EOC. Promotor hypomethylation at RASSF1A in OCSPCs from EOC tissues and changes to hypermethylation of EOC and OCSPCs from ascites could predict poor survival outcomes for EOC patients compared to without those changes of CCND2 and CDKN2B.
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Affiliation(s)
- Chih-Ming Ho
- Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General HospitalTaipei, Taiwan,School of Medicine, Fu Jen Catholic UniversityHsinchuang, New Taipei City, Taiwan,Department of Medical Research, Cathay General HospitalNew Taipei City, Taiwan
| | - Ting-Lin Yen
- Department of Medical Research, Cathay General HospitalNew Taipei City, Taiwan
| | - Tsai-Yen Chien
- Gynecologic Cancer Center, Department of Obstetrics and Gynecology, Cathay General HospitalTaipei, Taiwan
| | - Shih-Hung Huang
- Department of Pathology, Cathay General HospitalTaipei, Taiwan
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35
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Ratiometric Electrochemical Biosensing of Methyltransferase Activity. Catalysts 2022. [DOI: 10.3390/catal12111362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In this work, a novel ratiometric electrochemical readout platform was proposed and developed for the fast and flexible analysis of M.SssI methyltransferase (MTase) activity. In this platform, two hairpin DNAs (H1 and H2) were designed. H1 contains the palindromic sequence of 5′-CCGG-3′ in its stem which could be methylated and hybridize with H2 labeled by methylene blue (MB) as one of the signal reporters on a gold electrode (GE) in the presence of M.SssI MTase. Additionally, a specific immunoreaction was introduced by conjugating an anti-5-methylcytosine antibody, a DNA CpG methylation recognition unit, with 1,3-ferrocenedicarboxylic acid (Fc) as the second signal reporter. The results showed that when the Fc tag approaches, the MB tag was far from the gold electrode surface, resulting in a decrease in the oxidation peak current of MB (IMB) and an increase in the oxidation peak current of Fc (IFc). The ratiometric electrochemical method above shows the linear range of detection was 0 U/mL 40 U/mL with a detection limit of 0.083 U/mL (the mean signal of blank measures þ3s).
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CRISPR/dCas9-Dnmt3a-mediated targeted DNA methylation of APP rescues brain pathology in a mouse model of Alzheimer’s disease. Transl Neurodegener 2022; 11:41. [PMID: 36109806 PMCID: PMC9476342 DOI: 10.1186/s40035-022-00314-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 08/19/2022] [Indexed: 01/05/2023] Open
Abstract
Background Aberrant DNA methylation patterns have been observed in neurodegenerative diseases, including Alzheimer's disease (AD), and dynamic changes in DNA methylation are closely associated with the onset and progression of these diseases. Particularly, hypomethylation of the amyloid precursor protein gene (APP) has been reported in patients with AD. Methods In this study, we used catalytically inactivated Cas9 (dCas9) fused with Dnmt3a for targeted DNA methylation of APP, and showed that the CRISPR/dCas9-Dnmt3a-mediated DNA methylation system could efficiently induce targeted DNA methylation of APP both in vivo and in vitro. Results We hypothesized that the targeted methylation of the APP promoter might rescue AD-related neuronal cell death by reducing APP mRNA expression. The cultured APP-KI mouse primary neurons exhibited an altered DNA-methylation pattern on the APP promoter after dCas9-Dnmt3a treatment. Likewise, the APP mRNA level was significantly reduced in the dCas9-Dnmt3a-treated wild-type and APP-KI mouse primary neurons. We also observed decreased amyloid-beta (Aβ) peptide level and Aβ42/40 ratio in the dCas9-Dnmt3a-treated APP-KI mouse neurons compared to the control APP-KI mouse neurons. In addition, neuronal cell death was significantly decreased in the dCas9-Dnmt3a-treated APP-KI mouse neurons. Furthermore, the in vivo methylation of APP in the brain via dCas9-Dnmt3a treatment altered Aβ plaques and attenuated cognitive and behavioral impairments in the APP-KI mouse model. Conclusions These results suggest that the targeted methylation of APP via dCas9-Dnmt3a treatment can be a potential therapeutic strategy for AD. Supplementary Information The online version contains supplementary material available at 10.1186/s40035-022-00314-0.
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Li N, Wang L, Liang H, Lin C, Yi J, Yang Q, Luo H, Luo T, Zhang L, Li X, Wu K, Li F, Li N. Detecting and monitoring bladder cancer with exfoliated cells in urine. Front Oncol 2022; 12:986692. [PMID: 36158668 PMCID: PMC9491100 DOI: 10.3389/fonc.2022.986692] [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: 07/05/2022] [Accepted: 08/15/2022] [Indexed: 12/24/2022] Open
Abstract
Current methods for the diagnosis and monitoring of bladder cancer are invasive and have suboptimal sensitivity. Liquid biopsy as a non-invasive approach has been capturing attentions recently. To explore the ability of urine-based liquid biopsy in detecting and monitoring genitourinary tumors, we developed a method based on promoter-targeted DNA methylation of urine sediment DNA. We used samples from a primary bladder cancer cohort (n=40) and a healthy cohort (n=40) to train a model and obtained an integrated area under the curve (AUC) > 0.96 in the 10-fold cross-validation, which demonstrated the ability of our method for detecting bladder cancer from the healthy. We next validated the model with samples from a recurrent cohort (n=21) and a non-recurrent cohort (n=19) and obtained an AUC > 0.91, which demonstrated the ability of our model in monitoring the progress of bladder cancer. Moreover, 80% (4/5) of samples from patients with benign urothelial diseases had been considered to be healthy sample rather than cancer sample, preliminarily demonstrating the potential of distinguishing benign urothelial diseases from cancer. Further analysis basing on multiple-time point sampling revealed that the cancer signal in 80% (4/5) patients had decreased as expected when they achieved the recurrent-free state. All the results suggested that our method is a promising approach for noninvasive detection and prognostic monitoring of bladder cancer.
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Affiliation(s)
- Nannan Li
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Lei Wang
- Department of Urology, Peking University Shougang Hospital, Beijing, China
- Peking University Wu-jieping Urology Center, Peking University Health Science Center, Beijing, China
| | - Han Liang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Cong Lin
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Ji Yi
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Qin Yang
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Huijuan Luo
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Tian Luo
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
| | - Liwei Zhang
- Department of Urology, Peking University Shougang Hospital, Beijing, China
- Peking University Wu-jieping Urology Center, Peking University Health Science Center, Beijing, China
| | - Xiaojian Li
- Department of Urology, Peking University Shougang Hospital, Beijing, China
- Peking University Wu-jieping Urology Center, Peking University Health Science Center, Beijing, China
| | - Kui Wu
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- *Correspondence: Kui Wu, ; Fuqiang Li, ; Ningchen Li,
| | - Fuqiang Li
- Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- Guangdong Provincial Key Laboratory of Human Disease Genomics, Shenzhen Key Laboratory of Genomics, Beijing Genomics Institute (BGI)-Shenzhen, Shenzhen, China
- *Correspondence: Kui Wu, ; Fuqiang Li, ; Ningchen Li,
| | - Ningchen Li
- Department of Urology, Peking University Shougang Hospital, Beijing, China
- Peking University Wu-jieping Urology Center, Peking University Health Science Center, Beijing, China
- *Correspondence: Kui Wu, ; Fuqiang Li, ; Ningchen Li,
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Nengroo MA, Khan MA, Verma A, Datta D. Demystifying the CXCR4 conundrum in cancer biology: Beyond the surface signaling paradigm. Biochim Biophys Acta Rev Cancer 2022; 1877:188790. [PMID: 36058380 DOI: 10.1016/j.bbcan.2022.188790] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 10/14/2022]
Abstract
The oncogenic chemokine duo CXCR4-CXCL12/SDF-1 (C-X-C Receptor 4-C-X-C Ligand 12/ Stromal-derived factor 1) has been the topic of intense scientific disquisitions since Muller et al., in her ground-breaking research, described this axis as a critical determinant of organ-specific metastasis in breast cancer. Elevated CXCR4 levels correlate with distant metastases, poor prognosis, and unfavourable outcomes in most solid tumors. Therapeutic impediment of the axis in clinics with Food and Drug Administration (FDA) approved inhibitors like AMD3100 or Plerixafor yield dubious results, contrary to pre-clinical developments. Clinical trials entailing inhibition of CXCR7 (C-X-C Receptor 7), another convicted chemokine receptor that exhibits affinity for CXCL12, reveal outcomes analogous to that of CXCR4-CXCL12 axis blockade. Of note, the cellular CXCR4 knockout phenotype varies largely from that of inhibitor treatments. These shaky findings pique great curiosity to delve further into the realm of this infamous chemokine receptor to provide a probable explanation. A multitude of recent reports suggests the presence of an increased intracellular CXCR4 pool in various cancers, both cytoplasmic and nuclear. This intracellular CXCR4 protein reserve seems active as it correlates with vital tumor attributes, viz. prognosis, aggressiveness, metastasis, and disease-free survival. Diminishing this entire intracellular CXCR4 load apart from the surface signals looks encouraging from a therapeutic point of view. Transcending beyond the classically accepted concept of ligand-mediated surface signaling, this review sheds new light on plausible associations of intracellularly compartmentalised CXCR4 with various aspects of tumorigenesis. Besides, this review also puts forward a comprehensive account of CXCR4 regulation in different cancers.
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Affiliation(s)
- Mushtaq Ahmad Nengroo
- Division of Cancer Biology, CSIR-Central Drug Research Institute (CDRI), Lucknow-226031, India
| | - Muqtada Ali Khan
- Division of Cancer Biology, CSIR-Central Drug Research Institute (CDRI), Lucknow-226031, India
| | - Ayushi Verma
- Division of Cancer Biology, CSIR-Central Drug Research Institute (CDRI), Lucknow-226031, India
| | - Dipak Datta
- Division of Cancer Biology, CSIR-Central Drug Research Institute (CDRI), Lucknow-226031, India; Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh 201002, India.
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Baljinnyam T, Sowers ML, Hsu CW, Conrad JW, Herring JL, Hackfeld LC, Sowers LC. Chemical and enzymatic modifications of 5-methylcytosine at the intersection of DNA damage, repair, and epigenetic reprogramming. PLoS One 2022; 17:e0273509. [PMID: 36037209 PMCID: PMC9423628 DOI: 10.1371/journal.pone.0273509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 08/09/2022] [Indexed: 11/19/2022] Open
Abstract
The DNA of all living organisms is persistently damaged by endogenous reactions including deamination and oxidation. Such damage, if not repaired correctly, can result in mutations that drive tumor development. In addition to chemical damage, recent studies have established that DNA bases can be enzymatically modified, generating many of the same modified bases. Irrespective of the mechanism of formation, modified bases can alter DNA-protein interactions and therefore modulate epigenetic control of gene transcription. The simultaneous presence of both chemically and enzymatically modified bases in DNA suggests a potential intersection, or collision, between DNA repair and epigenetic reprogramming. In this paper, we have prepared defined sequence oligonucleotides containing the complete set of oxidized and deaminated bases that could arise from 5-methylcytosine. We have probed these substrates with human glycosylases implicated in DNA repair and epigenetic reprogramming. New observations reported here include: SMUG1 excises 5-carboxyuracil (5caU) when paired with A or G. Both TDG and MBD4 cleave 5-formyluracil and 5caU when mispaired with G. Further, TDG not only removes 5-formylcytosine and 5-carboxycytosine when paired with G, but also when mispaired with A. Surprisingly, 5caU is one of the best substrates for human TDG, SMUG1 and MBD4, and a much better substrate than T. The data presented here introduces some unexpected findings that pose new questions on the interactions between endogenous DNA damage, repair, and epigenetic reprogramming pathways.
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Affiliation(s)
- Tuvshintugs Baljinnyam
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Mark L. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Chia Wei Hsu
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- MD-PhD Combined Degree Program, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - James W. Conrad
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Jason L. Herring
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Linda C. Hackfeld
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Lawrence C. Sowers
- Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, Texas, United States of America
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, Texas, United States of America
- * E-mail:
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Brochet P, Ianni BM, Laugier L, Frade AF, Silva Nunes JP, Teixeira PC, Mady C, Ferreira LRP, Ferré Q, Santos RHB, Kuramoto A, Cabantous S, Steffen S, Stolf AN, Pomerantzeff P, Fiorelli AI, Bocchi EA, Pissetti CW, Saba B, Cândido DDS, Dias FC, Sampaio MF, Gaiotto FA, Marin-Neto JA, Fragata A, Zaniratto RCF, Siqueira S, Peixoto GDL, Rigaud VOC, Bacal F, Buck P, Almeida RR, Lin-Wang HT, Schmidt A, Martinelli M, Hirata MH, Donadi EA, Costa Pereira A, Rodrigues Junior V, Puthier D, Kalil J, Spinelli L, Cunha-Neto E, Chevillard C. Epigenetic regulation of transcription factor binding motifs promotes Th1 response in Chagas disease cardiomyopathy. Front Immunol 2022; 13:958200. [PMID: 36072583 PMCID: PMC9441916 DOI: 10.3389/fimmu.2022.958200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/26/2022] [Indexed: 01/03/2023] Open
Abstract
Chagas disease, caused by the protozoan Trypanosoma cruzi, is an endemic parasitic disease of Latin America, affecting 7 million people. Although most patients are asymptomatic, 30% develop complications, including the often-fatal Chronic Chagasic Cardiomyopathy (CCC). Although previous studies have demonstrated some genetic deregulations associated with CCCs, the causes of their deregulations remain poorly described. Based on bulk RNA-seq and whole genome DNA methylation data, we investigated the genetic and epigenetic deregulations present in the moderate and severe stages of CCC. Analysis of heart tissue gene expression profile allowed us to identify 1407 differentially expressed transcripts (DEGs) specific from CCC patients. A tissue DNA methylation analysis done on the same tissue has permitted the identification of 92 regulatory Differentially Methylated Regions (DMR) localized in the promoter of DEGs. An in-depth study of the transcription factors binding sites (TFBS) in the DMRs corroborated the importance of TFBS’s DNA methylation for gene expression in CCC myocardium. TBX21, RUNX3 and EBF1 are the transcription factors whose binding motif appears to be affected by DNA methylation in the largest number of genes. By combining both transcriptomic and methylomic analysis on heart tissue, and methylomic analysis on blood, 4 biological processes affected by severe CCC have been identified, including immune response, ion transport, cardiac muscle processes and nervous system. An additional study on blood methylation of moderate CCC samples put forward the importance of ion transport and nervous system in the development of the disease.
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Affiliation(s)
- Pauline Brochet
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Barbara Maria Ianni
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Laurie Laugier
- Aix Marseille Université, Génétique et Immunologie des Maladies Parasitaires, Inserm, UMR_906, Marseille, France
| | - Amanda Farage Frade
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - João Paulo Silva Nunes
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Priscila Camillo Teixeira
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Charles Mady
- Myocardiopathies and Aortic Diseases Unit, Heart Institute Instituto do Coração (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Ludmila Rodrigues Pinto Ferreira
- RNA Systems Biology Laboratory (RSBL), Departamento de Morfologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Quentin Ferré
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Ronaldo Honorato Barros Santos
- Division of Transplantation, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Andreia Kuramoto
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Sandrine Cabantous
- Aix Marseille Université, Génétique et Immunologie des Maladies Parasitaires, Inserm, UMR_906, Marseille, France
| | - Samuel Steffen
- Division of Transplantation, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Surgery, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Antonio Noedir Stolf
- Division of Surgery, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Pablo Pomerantzeff
- Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Alfredo Inacio Fiorelli
- Division of Surgery, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Edimar Alcides Bocchi
- Division of Surgery, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Cristina Wide Pissetti
- Laboratory of Immunology, Universidade Federal Do Triângulo Mineiro (UFTM), Uberaba, Brazil
| | - Bruno Saba
- Laboratório de Investigação Molecular em Cardiologia, Instituto de Cardiologia Dante Pazzanese (IDPC), São Paulo, Brazil
| | - Darlan da Silva Cândido
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Fabrício C. Dias
- School of Medicine of Ribeirão Preto Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, Brazil
| | - Marcelo Ferraz Sampaio
- Laboratório de Investigação Molecular em Cardiologia, Instituto de Cardiologia Dante Pazzanese (IDPC), São Paulo, Brazil
| | - Fabio Antônio Gaiotto
- Division of Transplantation, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Surgery, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - José Antonio Marin-Neto
- School of Medicine of Ribeirão Preto Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, Brazil
| | - Abílio Fragata
- Laboratório de Investigação Molecular em Cardiologia, Instituto de Cardiologia Dante Pazzanese (IDPC), São Paulo, Brazil
| | - Ricardo Costa Fernandes Zaniratto
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Sergio Siqueira
- Pacemaker Clinic, Heart Institute Instituto do Coração (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Giselle De Lima Peixoto
- Pacemaker Clinic, Heart Institute Instituto do Coração (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Vagner Oliveira-Carvalho Rigaud
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Heart Failure Unit, Heart Institute Instituto do Coração (InCor) School of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Fernando Bacal
- Division of Transplantation, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
| | - Paula Buck
- Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Rafael Ribeiro Almeida
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Hui Tzu Lin-Wang
- Laboratório de Investigação Molecular em Cardiologia, Instituto de Cardiologia Dante Pazzanese (IDPC), São Paulo, Brazil
| | - André Schmidt
- School of Medicine of Ribeirão Preto Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, Brazil
| | - Martino Martinelli
- Pacemaker Clinic, Heart Institute Instituto do Coração (InCor), School of Medicine, University of São Paulo, São Paulo, Brazil
| | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, Faculty of Pharmaceutical Sciences, University of São Paulo (USP), São Paulo, Brazil
| | - Eduardo Antonio Donadi
- School of Medicine of Ribeirão Preto Faculdade de Medicina de Ribeirão Preto (FMRP), University of São Paulo, Ribeirão Preto, Brazil
| | - Alexandre Costa Pereira
- Heart Institute (InCor), School of Medicine, University of São Paulo, São Paulo, São Paulo, Brazil
| | | | - Denis Puthier
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
| | - Jorge Kalil
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
| | - Lionel Spinelli
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
- Aix Marseille Université, CNRS, INSERM, Centre d'Immunologie de Marseille-Luminy, Marseille, France
- *Correspondence: Christophe Chevillard, ; Edecio Cunha-Neto, ; Lionel Spinelli,
| | - Edecio Cunha-Neto
- Laboratory of Immunology, Heart Institute Instituto do Coração (InCor), University of São Paulo, School of Medicine, São Paulo, Brazil
- Division of Clinical Immunology and Allergy, University of São Paulo, School of Medicine, São Paulo, Brazil
- Instituto Nacional de Ciência e Tecnologia, INCT, III- Institute for Investigation in Immunology, São Paulo, Brazil
- *Correspondence: Christophe Chevillard, ; Edecio Cunha-Neto, ; Lionel Spinelli,
| | - Christophe Chevillard
- Institut National de la Santé Et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR)_1090, Aix Marseille Université, TAGC Theories and Approaches of Genomic Complexity, Institut MarMaRa, Marseille, France
- *Correspondence: Christophe Chevillard, ; Edecio Cunha-Neto, ; Lionel Spinelli,
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Epigenetic regulation of fetal brain development in pig. Gene 2022; 844:146823. [PMID: 35988784 DOI: 10.1016/j.gene.2022.146823] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 07/27/2022] [Accepted: 08/15/2022] [Indexed: 02/01/2023]
Abstract
How fetal brain development is regulated at the molecular level is not well understood. Due to ethical challenges associated with research on the human fetus, large animals particularly pigs are increasingly used to study development and disorders of fetal brain. The pig fetal brain grows rapidly during the last ∼ 50 days before birth which is around day 60 (d60) of pig gestation. But what regulates the onset of accelerated growth of the brain is unknown. The current study tests the hypothesis that epigenetic alteration around d60 is involved in the onset of rapid growth of fetal brain of pig. To test this hypothesis, DNA methylation changes of fetal brain was assessed in a genome-wide manner by Enzymatic Methyl-seq (EM-seq) during two gestational periods (GP): d45 vs. d60 (GP1) and d60 vs. d90 (GP2). The cytosine-guanine (CpG) methylation data was analyzed in an integrative manner with the RNA-seq data generated from the same brain samples from our earlier study. A neural network based modeling approach was implemented to learn changes in methylation patterns of the differentially expressed genes, and then predict methylations of the brain in a genome-wide manner during rapid growth. This approach identified specific methylations that changed in a mutually informative manner during rapid growth of the fetal brain. These methylations were significantly overrepresented in specific genic as well as intergenic features including CpG islands, introns, and untranslated regions. In addition, sex-bias methylations of known single nucleotide polymorphic sites were also identified in the fetal brain ide during rapid growth.
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Gupta A, Nair S. Heritable Epigenomic Modifications Influence Stress Resilience and Rapid Adaptations in the Brown Planthopper ( Nilaparvata lugens). Int J Mol Sci 2022; 23:8728. [PMID: 35955860 PMCID: PMC9368798 DOI: 10.3390/ijms23158728] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/25/2022] Open
Abstract
DNA methylation in insects is integral to cellular differentiation, development, gene regulation, genome integrity, and phenotypic plasticity. However, its evolutionary potential and involvement in facilitating rapid adaptations in insects are enigmatic. Moreover, our understanding of these mechanisms is limited to a few insect species, of which none are pests of crops. Hence, we studied methylation patterns in the brown planthopper (BPH), a major rice pest, under pesticide and nutritional stress, across its life stages. Moreover, as the inheritance of epigenetic changes is fundamentally essential for acclimation, adaptability, and evolution, we determined the heritability and persistence of stress-induced methylation marks in BPH across generations. Our results revealed that DNA methylation pattern(s) in BPH varies/vary with environmental cues and is/are insect life-stage specific. Further, our findings provide novel insights into the heritability of stress-induced methylation marks in BPH. However, it was observed that, though heritable, these marks eventually fade in the absence of the stressors, thereby suggesting the existence of fitness cost(s) associated with the maintenance of the stressed epigenotype. Furthermore, we demonstrate how 5-azacytidine-mediated disruption of BPH methylome influences expression levels of stress-responsive genes and, thereby, highlight demethylation/methylation as a phenomenon underlying stress resilience of BPH.
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Affiliation(s)
| | - Suresh Nair
- Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India
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Agborbesong E, Li LX, Li L, Li X. Molecular Mechanisms of Epigenetic Regulation, Inflammation, and Cell Death in ADPKD. Front Mol Biosci 2022; 9:922428. [PMID: 35847973 PMCID: PMC9277309 DOI: 10.3389/fmolb.2022.922428] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder, which is caused by mutations in the PKD1 and PKD2 genes, characterizing by progressive growth of multiple cysts in the kidneys, eventually leading to end-stage kidney disease (ESKD) and requiring renal replacement therapy. In addition, studies indicate that disease progression is as a result of a combination of factors. Understanding the molecular mechanisms, therefore, should facilitate the development of precise therapeutic strategies for ADPKD treatment. The roles of epigenetic modulation, interstitial inflammation, and regulated cell death have recently become the focuses in ADPKD. Different epigenetic regulators, and the presence of inflammatory markers detectable even before cyst growth, have been linked to cyst progression. Moreover, the infiltration of inflammatory cells, such as macrophages and T cells, have been associated with cyst growth and deteriorating renal function in humans and PKD animal models. There is evidence supporting a direct role of the PKD gene mutations to the regulation of epigenetic mechanisms and inflammatory response in ADPKD. In addition, the role of regulated cell death, including apoptosis, autophagy and ferroptosis, have been investigated in ADPKD. However, there is no consensus whether cell death promotes or delays cyst growth in ADPKD. It is therefore necessary to develop an interactive picture between PKD gene mutations, the epigenome, inflammation, and cell death to understand why inherited PKD gene mutations in patients may result in the dysregulation of these processes that increase the progression of renal cyst formation.
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Affiliation(s)
- Ewud Agborbesong
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Linda Xiaoyan Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Lu Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
| | - Xiaogang Li
- Department of Internal Medicine, Mayo Clinic, Rochester, MN, United States.,Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, United States
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Zhao Q, Hu W, Xu J, Zeng S, Xi X, Chen J, Wu X, Hu S, Zhong T. Comprehensive Pan-Cancer Analysis of Senescence With Cancer Prognosis and Immunotherapy. Front Mol Biosci 2022; 9:919274. [PMID: 35911954 PMCID: PMC9334796 DOI: 10.3389/fmolb.2022.919274] [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: 04/13/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Senescence is a double-edged sword in tumorigenesis and affects the immunotherapy response through the modulation of the host’s immune system. However, there is currently a lack of comprehensive analysis of the senescence-related genes (SRGs) in human cancers, and the predictive role of senescence in cancer immunotherapy response has not been explored. The multi-omics approaches were performed in this article to conduct a systematic pan-cancer genomic analysis of SRGs in cancer. In addition, we calculated the generic senescence score (SS) to quantify the senescence levels in cancers and explored the correlations of SS with cancer prognosis, biological processes, and tumor microenvironment (TME). The gene signatures were deregulated in multiple cancers and indicated a context-dependent correlation with prognosis, tumor-immune evasion, and response to therapy across various tumor types. Further analysis disclosed that SS was positively associated with the infiltration levels of immune suppressive cells, including induced Tregs (iTregs), central memory Ts (Tcms), and natural Tregs (nTregs), and negatively associated with immune killer cells, including natural killers (NKs) and mucosal-associated invariant Ts (MAITs). Moreover, the SS was significantly correlated with tumor-associated macrophages (TAMs), cancer-associated fibroblasts (CAFs), immune-related genes, and immune checkpoints and had a predictive value of immunotherapy response. Thus, the expression of SRGs was involved in resistance to several anticancer drugs. Our work illustrates the characterization of senescence across various malignancies and highlights the potential of senescence as a biomarker of the response to immunotherapy.
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Affiliation(s)
- Qinfei Zhao
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Weiquan Hu
- Department of Joint Surgery, Ganzhou People’s Hospital, Ganzhou, China
| | - Jing Xu
- Department of Orthopaedic Surgery, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Shaoying Zeng
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xuxiang Xi
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Jing Chen
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Xiangsheng Wu
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Suping Hu
- Department of Emergency, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
| | - Tianyu Zhong
- Department of Laboratory Medicine, First Affiliated Hospital of Gannan Medical University, Ganzhou, China
- *Correspondence: Tianyu Zhong,
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45
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Chilunga FP, Meeks KAC, Henneman P, Agyemang C, Doumatey AP, Rotimi CN, Adeyemo AA. An epigenome-wide association study of insulin resistance in African Americans. Clin Epigenetics 2022; 14:88. [PMID: 35836279 PMCID: PMC9281172 DOI: 10.1186/s13148-022-01309-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 07/04/2022] [Indexed: 11/18/2022] Open
Abstract
Background African Americans have a high risk for type 2 diabetes (T2D) and insulin resistance. Studies among other population groups have identified DNA methylation loci associated with insulin resistance, but data in African Americans are lacking. Using DNA methylation profiles of blood samples obtained from the Illumina Infinium® HumanMethylation450 BeadChip, we performed an epigenome-wide association study to identify DNA methylation loci associated with insulin resistance among 136 non-diabetic, unrelated African American men (mean age 41.6 years) from the Howard University Family Study. Results We identified three differentially methylated positions (DMPs) for homeostatic model assessment of insulin resistance (HOMA-IR) at 5% FDR. One DMP (cg14013695, HOXA5) is a known locus among Mexican Americans, while the other two DMPs are novel—cg00456326 (OSR1; beta = 0.027) and cg20259981 (ST18; beta = 0.010). Although the cg00456326 DMP is novel, the OSR1 gene has previously been found associated with both insulin resistance and T2D in Europeans. The genes HOXA5 and ST18 have been implicated in biological processes relevant to insulin resistance. Differential methylation at the significant HOXA5 and OSR1 DMPs is associated with differences in gene expression in the iMETHYL database. Analysis of differentially methylated regions (DMRs) did not identify any epigenome-wide DMRs for HOMA-IR. We tested transferability of HOMA-IR associated DMPs from five previous EWAS in Mexican Americans, Indian Asians, Europeans, and European ancestry Americans. Out of the 730 previously reported HOMA-IR DMPs, 47 (6.4%) were associated with HOMA-IR in this cohort of African Americans. Conclusions The findings from our study suggest substantial differences in DNA methylation patterns associated with insulin resistance across populations. Two of the DMPs we identified in African Americans have not been reported in other populations, and we found low transferability of HOMA-IR DMPs reported in other populations in African Americans. More work in African-ancestry populations is needed to confirm our findings as well as functional analyses to understand how such DNA methylation alterations contribute to T2D pathology. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01309-4.
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Affiliation(s)
- Felix P Chilunga
- Department of Public & Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Karlijn A C Meeks
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Peter Henneman
- Department of Human Genetics, Amsterdam Reproduction & Development Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Charles Agyemang
- Department of Public & Occupational Health, Amsterdam Public Health Research Institute, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, The Netherlands
| | - Ayo P Doumatey
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Charles N Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
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Di Lena P, Sala C, Nardini C. Evaluation of different computational methods for DNA methylation-based biological age. Brief Bioinform 2022; 23:6632619. [PMID: 35794713 DOI: 10.1093/bib/bbac274] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/27/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
In recent years there has been a widespread interest in researching biomarkers of aging that could predict physiological vulnerability better than chronological age. Aging, in fact, is one of the most relevant risk factors for a wide range of maladies, and molecular surrogates of this phenotype could enable better patients stratification. Among the most promising of such biomarkers is DNA methylation-based biological age. Given the potential and variety of computational implementations (epigenetic clocks), we here present a systematic review of such clocks. Furthermore, we provide a large-scale performance comparison across different tissues and diseases in terms of age prediction accuracy and age acceleration, a measure of deviance from physiology. Our analysis offers both a state-of-the-art overview of the computational techniques developed so far and a heterogeneous picture of performances, which can be helpful in orienting future research.
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Affiliation(s)
- Pietro Di Lena
- Department of Computer Science and Engineering, University of Bologna, Mura Anteo Zamboni 7, 40126 Bologna, Italy
| | - Claudia Sala
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Via Massarenti 9, 40138, Bologna, Italy
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CpG Methylation Altered the Stability and Structure of the i-Motifs Located in the CpG Islands. Int J Mol Sci 2022; 23:ijms23126467. [PMID: 35742916 PMCID: PMC9223787 DOI: 10.3390/ijms23126467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 11/25/2022] Open
Abstract
Cytosine methylation within the 5′-C-phosphate-G-3′ sequence of nucleotides (called CpG methylation) is a well-known epigenetic modification of genomic DNA that plays an important role in gene expression and development. CpG methylation is likely to be altered in the CpG islands. CpG islands are rich in cytosine, forming a structure called the i-motif via cytosine-cytosine hydrogen bonding. However, little is known about the effect of CpG methylation on the i-motif. In this study, The CpG methylation-induced structural changes on the i-motif was examined by thermal stability, circular dichroism (CD) spectroscopy, and native-polyacrylamide gel electrophoresis (Native-PAGE) evaluation of five i-motif-forming DNAs from four cancer-related genes (VEGF, C-KIT, BCL2, and HRAS). This research shows that CpG methylation increased the transitional pH of several i-motif-forming DNAs and their thermal stability. When examining the effect of CpG methylation on the i-motif in the presence of opposite G4-forming DNAs, CpG methylation influenced the proportion of G4 and i-motif formation. This study showed that CpG methylation altered the stability and structure of the i-motif in CpG islands.
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Clothier JL, Grooms AN, Porter-Gill PA, Gill PS, Schaefer GB. Identification of DCAF1 by Clinical Exome Sequencing and Methylation Analysis as a Candidate Gene for Autism and Intellectual Disability: A Case Report. J Pers Med 2022; 12:jpm12060886. [PMID: 35743672 PMCID: PMC9224943 DOI: 10.3390/jpm12060886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/14/2022] [Accepted: 05/25/2022] [Indexed: 11/16/2022] Open
Abstract
Autism spectrum disorder (ASD) comprises a heterogeneous group of neurodevelopmental disorders and occurs in all racial, ethnic, and socioeconomic groups. Cutting-edge technologies are contributing to understanding genetic underpinnings in ASD. The reported patient is a 32-year-old male and as an infant was noted to have microcephaly, hypospadias, pulmonary vascular anomaly, and small stature. He was diagnosed with Cornelia De Lange Syndrome (CDLS) at that time based on the clinical features. As a child, he had autistic features and intellectual disabilities and as diagnoses with autism and intellectual disability. He was referred as an adult to our neurodiversity clinic and a full exome trio sequencing with reflex to mitochondrial genes identified a de novo variant of uncertain significance in a candidate gene, DCAF1. The specific variant was c.137 C > T (p.Thr46Ile) in exon 4 in the DCAF1 gene. In silico analysis supports a deleterious effect on protein structure/function. DCAF1 participates with DDB1 and CUL4 as a part of the E3 ubiquitin ligase complex. The E3 ligase complex has been associated with a syndromic form of X-linked intellectual disability. The DDB1/CUL4 E3 ubiquitination complex plays a role in methylation-dependent ubiquitination. Next, a methylation study identified a signature similar to the methylation pattern found in X- linked intellectual disability type 93. This is associated with variants of the BRWD3 gene, which is linked with the functioning of the DDB1/CUL4 E3 ubiquitination complex. Taken together, this suggests that the de novo DCAF1 variant may be a newly identified molecular cause of autism and intellectual disability.
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Affiliation(s)
- Jeffery L. Clothier
- Psychiatric Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
- Correspondence: ; Tel.: +001-501-526-8100
| | - Amy N. Grooms
- Psychiatric Research Institute, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | | | - Pritmohinder S. Gill
- Department of Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
| | - G. Bradley Schaefer
- Genetics and Pediatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72202, USA;
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de Krijger M, Hageman IL, Li Yim AYF, Verhoeff J, Garcia Vallejo JJ, van Hamersveld PHP, Levin E, Hakvoort TBM, Wildenberg ME, Henneman P, Ponsioen CY, de Jonge WJ. Epigenetic Signatures Discriminate Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis From Patients With Ulcerative Colitis. Front Immunol 2022; 13:840935. [PMID: 35371111 PMCID: PMC8965896 DOI: 10.3389/fimmu.2022.840935] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/14/2022] [Indexed: 12/12/2022] Open
Abstract
Background Primary sclerosing cholangitis (PSC) is a chronic inflammatory liver disease affecting the intra- and extrahepatic bile ducts, and is strongly associated with ulcerative colitis (UC). In this study, we explored the peripheral blood DNA methylome and its immune cell composition in patients with PSC-UC, UC, and healthy controls (HC) with the aim to develop a predictive assay in distinguishing patients with PSC-UC from those with UC alone. Methods The peripheral blood DNA methylome of male patients with PSC and concomitant UC, UC and HCs was profiled using the Illumina HumanMethylation Infinium EPIC BeadChip (850K) array. Differentially methylated CpG position (DMP) and region (DMR) analyses were performed alongside gradient boosting classification analyses to discern PSC-UC from UC patients. As observed differences in the DNA methylome could be the result of differences in cellular populations, we additionally employed mass cytometry (CyTOF) to characterize the immune cell compositions. Results Genome wide methylation analysis did not reveal large differences between PSC-UC and UC patients nor HCs. Nonetheless, using gradient boosting we were capable of discerning PSC-UC from UC with an area under the receiver operator curve (AUROC) of 0.80. Four CpG sites annotated to the NINJ2 gene were found to strongly contribute to the predictive performance. While CyTOF analyses corroborated the largely similar blood cell composition among patients with PSC-UC, UC and HC, a higher abundance of myeloid cells was observed in UC compared to PSC-UC patients. Conclusion DNA methylation enables discerning PSC-UC from UC patients, with a potential for biomarker development.
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Affiliation(s)
- Manon de Krijger
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Ishtu L Hageman
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Andrew Y F Li Yim
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Jan Verhoeff
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Molecular Cell Biology and Immunology, Amsterdam Infection & Immunity and Cancer Center Amsterdam, Amsterdam University Medical Centers, Free University of Amsterdam, Amsterdam, Netherlands
| | - Juan J Garcia Vallejo
- Department of Molecular Cell Biology and Immunology, Amsterdam Infection & Immunity and Cancer Center Amsterdam, Amsterdam University Medical Centers, Free University of Amsterdam, Amsterdam, Netherlands
| | - Patricia H P van Hamersveld
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Evgeni Levin
- Department of Vascular Medicine, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Horaizon BV, Delft, Netherlands
| | - Theodorus B M Hakvoort
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Manon E Wildenberg
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Peter Henneman
- Department of Clinical Genetics, Genome Diagnostics Laboratory, Amsterdam Reproduction and Development, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Cyriel Y Ponsioen
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands
| | - Wouter J de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism, Amsterdam University Medical Centers, University of Amsterdam, Amsterdam, Netherlands.,Department of Surgery, University Clinic of Bonn, Bonn, Germany
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50
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Alsayed RKME, Khan AQ, Ahmad F, Ansari AW, Alam MA, Buddenkotte J, Steinhoff M, Uddin S, Ahmad A. Epigenetic Regulation of CXCR4 Signaling in Cancer Pathogenesis and Progression. Semin Cancer Biol 2022; 86:697-708. [PMID: 35346802 DOI: 10.1016/j.semcancer.2022.03.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/18/2022] [Accepted: 03/21/2022] [Indexed: 02/08/2023]
Abstract
Signaling involving chemokine receptor CXCR4 and its ligand SDF-1/CXL12 has been investigated for many years for its possible role in cancer progression and pathogenesis. Evidence emerging from clinical studies in recent years has further established diagnostic as well as prognostic importance of CXCR4 signaling. CXCR4 and SDF-1 are routinely reported to be elevated in tumors, distant metastases, which correlates with poor survival of patients. These findings have kindled interest in the mechanisms that regulate CXCR4/SDF-1 expression. Of note, there is a particular interest in the epigenetic regulation of CXCR4 signaling that may be responsible for upregulated CXCR4 in primary as well as metastatic cancers. This review first lists the clinical evidence supporting CXCR4 signaling as putative cancer diagnostic and/or prognostic biomarker, followed by a discussion on reported epigenetic mechanisms that affect CXCR4 expression. These mechanisms include regulation by non-coding RNAs, such as, microRNAs, long non-coding RNAs and circular RNAs. Additionally, we also discuss the regulation of CXCR4 expression through methylation and acetylation. Better understanding and appreciation of epigenetic regulation of CXCR4 signaling can invariably lead to identification of novel therapeutic targets as well as therapies to regulate this oncogenic signaling.
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Affiliation(s)
- Reem Khaled M E Alsayed
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Abdul Q Khan
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Fareed Ahmad
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Abdul Wahid Ansari
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Majid Ali Alam
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Jorg Buddenkotte
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar
| | - Martin Steinhoff
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar; Weill Cornell Medicine-Qatar, Medical School, Doha, 24144, Qatar; Dept. of Dermatology, Weill Cornell Medicine, New York, 10065, NY, USA
| | - Shahab Uddin
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Laboratory Animal Research Center, Qatar University, Doha, 2713, Qatar
| | - Aamir Ahmad
- Translational Research Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Dermatology Institute, Academic Health System, Hamad Medical Corporation, Doha, 3050, Qatar; Department of Dermatology and Venereology, Rumailah Hospital, Hamad Medical Corporation, Doha, 3050, Qatar.
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