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Article: 10 Years of Toxicogenomics section in Frontiers in Genetics: Past discoveries and Future Perspectives.

Ruden, Douglas M

2022 Volume 13, Page(s) 979761

Abstract: The Frontiers Media family has over 200 journals, which are each headed by usually one Field Chief Editor, and several thousand specialty sections, which are each headed by one or more Specialty Chief Editors. The year 2021 was the 10th anniversary of ... ...

Abstract	The Frontiers Media family has over 200 journals, which are each headed by usually one Field Chief Editor, and several thousand specialty sections, which are each headed by one or more Specialty Chief Editors. The year 2021 was the 10th anniversary of the founding of the Frontiers in Genetics journal and the Frontiers in Toxicogenomics specialty section of this journal. In 2021, we also announce one of the newest of the Frontiers journals-Frontiers in Toxicology which is part of the Frontiers Media family of journals but independent of Frontiers in Genetics. Dr. Ruden is the founding, and currently sole, Specialty Chief Editor of Frontiers in Toxicogenomics and one of 9 Specialty Chief Editors of Frontiers in Toxicology. As of 2021, Frontiers in Toxicogenomics has published over 138 articles and has over 370 Editors including 90 Associate Editors and 280 Review Editors. The Frontiers in Genetics impact factor was initially approximately 2.5 when it was first listed in PubMed in 2015 and has risen steadily to its current value of 4.8, which is typical for the majority of the over 200 Frontiers journals that have established impact factors. In this overview of the first decade of Frontiers in Toxicogenomics, we discuss the top 5 articles with the highest Scopus citations, which were all written in the first few years of the journal. The article with the highest number of citations, with 353 Scopus over 600 Google Scholar citations, and the highest average number of citations (67) that steadily increased from 10 citations in 2013 to 119 citations in 2021, was written in 2012 by Dr. Ruden's laboratory and titled, "Using
Language	English
Publishing date	2022-09-12
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.979761
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Editorial: Insights in epigenomics and epigenetics: 2022.

Ruden, Douglas M / Rastegar, Mojgan

Frontiers in genetics

2023 Volume 14, Page(s) 1205975

Language	English
Publishing date	2023-06-13
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2023.1205975
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Pathological epigenetic events and reversibility review: the intersection between hallmarks of aging and developmental origin of health and disease.

Ruden, Douglas M / Singh, Aditi / Rappolee, Daniel A

Epigenomics

2023 Volume 15, Issue 14, Page(s) 741–754

Abstract: We discuss pathological epigenetic events that are reversible (PEERs). A recent study by Poganik and colleagues showed that severe stress in mice and humans transiently elevates biological age of several tissues, and this transient age increase is ... ...

Abstract	We discuss pathological epigenetic events that are reversible (PEERs). A recent study by Poganik and colleagues showed that severe stress in mice and humans transiently elevates biological age of several tissues, and this transient age increase is reversible when the stress is removed. These studies suggest new strategies for reversing normal aging. However, it is important to note that developmental origin of health and disease studies have shown that developmental exposure to toxic chemicals such as lead causes permanent changes in neuron shape, connectivity and cellular hyperplasia of organs such as the heart and liver. In this review, the PEER hypothesis speculates that the hallmarks of aging and the hallmarks of developmental origin of health and disease intersect at PEERs.
MeSH term(s)	Humans ; Animals ; Mice ; Aging/genetics ; Epigenomics ; Heart ; Liver ; Epigenesis, Genetic
Language	English
Publishing date	2023-09-05
Publishing country	England
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	2537199-X
ISSN	1750-192X ; 1750-1911
ISSN (online)	1750-192X
ISSN	1750-1911
DOI	10.2217/epi-2023-0224
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Epigenetic Reprogramming in

Singh, Aditi / Rappolee, Daniel A / Ruden, Douglas M

Cells

2023 Volume 12, Issue 14

Abstract: In this review, advances in the understanding of epigenetic reprogramming from fertilization to the development of primordial germline cells in a mouse ... ...

Abstract	In this review, advances in the understanding of epigenetic reprogramming from fertilization to the development of primordial germline cells in a mouse and
MeSH term(s)	Male ; Female ; Humans ; Mice ; Animals ; Epigenesis, Genetic ; Cell Differentiation ; Germ Cells ; Fertilization ; DNA ; Mammals
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2023-07-17
Publishing country	Switzerland
Document type	Journal Article ; Review ; Research Support, N.I.H., Extramural
ZDB-ID	2661518-6
ISSN	2073-4409 ; 2073-4409
ISSN (online)	2073-4409
ISSN	2073-4409
DOI	10.3390/cells12141874
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Biological Aging Acceleration Due to Environmental Exposures: An Exciting New Direction in Toxicogenomics Research.

Dutta, Sudipta / Goodrich, Jaclyn M / Dolinoy, Dana C / Ruden, Douglas M

Genes

2023 Volume 15, Issue 1

Abstract: Biological clock technologies are designed to assess the acceleration of biological age (B-age) in diverse cell types, offering a distinctive opportunity in toxicogenomic research to explore the impact of environmental stressors, social challenges, and ... ...

Abstract	Biological clock technologies are designed to assess the acceleration of biological age (B-age) in diverse cell types, offering a distinctive opportunity in toxicogenomic research to explore the impact of environmental stressors, social challenges, and unhealthy lifestyles on health impairment. These clocks also play a role in identifying factors that can hinder aging and promote a healthy lifestyle. Over the past decade, researchers in epigenetics have developed testing methods that predict the chronological and biological age of organisms. These methods rely on assessing DNA methylation (DNAm) levels at specific CpG sites, RNA levels, and various biomolecules across multiple cell types, tissues, and entire organisms. Commonly known as 'biological clocks' (B-clocks), these estimators hold promise for gaining deeper insights into the pathways contributing to the development of age-related disorders. They also provide a foundation for devising biomedical or social interventions to prevent, reverse, or mitigate these disorders. This review article provides a concise overview of various epigenetic clocks and explores their susceptibility to environmental stressors.
MeSH term(s)	Toxicogenetics ; DNA Methylation ; Epigenesis, Genetic
Language	English
Publishing date	2023-12-21
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes15010016
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Sex-Differences in Traumatic Brain Injury in the Absence of Tau in

Shah, Ekta J / Gurdziel, Katherine / Ruden, Douglas M

Genes

2021 Volume 12, Issue 6

Abstract: Traumatic brain injuries, a leading cause of death and disability worldwide, are caused by a severe impact to the head that impairs physiological and psychological function. In addition to severity, type and brain area affected, brain injury outcome is ... ...

Abstract	Traumatic brain injuries, a leading cause of death and disability worldwide, are caused by a severe impact to the head that impairs physiological and psychological function. In addition to severity, type and brain area affected, brain injury outcome is also influenced by the biological sex of the patient. Traumatic brain injury triggers accumulation of Tau protein and the subsequent development of Tauopathies, including Alzheimer's disease and Chronic traumatic encephalopathy. Recent studies report differences in Tau network connections between healthy males and females, but the possible role of Tau in sex-dependent outcome to brain injury is unclear. Thus, we aimed to determine if Tau ablation would alleviate sex dependent outcomes in injured flies. We first assessed motor function and survival in
MeSH term(s)	Animals ; Brain/metabolism ; Brain Injuries, Traumatic/genetics ; Brain Injuries, Traumatic/metabolism ; Drosophila Proteins/deficiency ; Drosophila Proteins/genetics ; Drosophila melanogaster ; Female ; Male ; Movement ; Sex Factors ; Transcriptome ; tau Proteins/deficiency ; tau Proteins/genetics
Chemical Substances	Drosophila Proteins ; tau Proteins ; tau protein, Drosophila
Language	English
Publishing date	2021-06-14
Publishing country	Switzerland
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2527218-4
ISSN	2073-4425 ; 2073-4425
ISSN (online)	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12060917
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Sex-Differences in Traumatic Brain Injury in the Absence of Tau in Drosophila

Shah, Ekta J. / Gurdziel, Katherine / Ruden, Douglas M.

Genes. 2021 June 14, v. 12, no. 6

2021

Abstract	Traumatic brain injuries, a leading cause of death and disability worldwide, are caused by a severe impact to the head that impairs physiological and psychological function. In addition to severity, type and brain area affected, brain injury outcome is also influenced by the biological sex of the patient. Traumatic brain injury triggers accumulation of Tau protein and the subsequent development of Tauopathies, including Alzheimer’s disease and Chronic traumatic encephalopathy. Recent studies report differences in Tau network connections between healthy males and females, but the possible role of Tau in sex-dependent outcome to brain injury is unclear. Thus, we aimed to determine if Tau ablation would alleviate sex dependent outcomes in injured flies. We first assessed motor function and survival in tau knock-out flies and observed sex-differences in climbing ability, but no change in locomotor activity in either sex post-injury. Sex differences in survival time were also observed in injured tau deficient flies with a dramatically higher percent of female death within 24 h than males. Additionally, 3′mRNA-Seq studies in isolated fly brains found that tau deficient males show more gene transcript changes than females post-injury. Our results suggest that sex differences in TBI outcome and recovery are not dependent on the presence of Tau in Drosophila.
Keywords	Drosophila ; brain ; brain damage ; death ; encephalopathy ; females ; head ; locomotion ; messenger RNA ; patients
Language	English
Dates of publication	2021-0614
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes12060917
Database	NAL-Catalogue (AGRICOLA)

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Article: Drosophila

Shah, Ekta J / Gurdziel, Katherine / Ruden, Douglas M

Frontiers in neurology

2020 Volume 11, Page(s) 511

Abstract: Every year, millions of people in the US suffer brain damage from mild to severe traumatic brain injuries (TBI) that result from a sudden impact to the head. Despite TBI being a leading cause of death and disability worldwide, sex differences that ... ...

Abstract	Every year, millions of people in the US suffer brain damage from mild to severe traumatic brain injuries (TBI) that result from a sudden impact to the head. Despite TBI being a leading cause of death and disability worldwide, sex differences that contribute to varied outcomes post-injury are not extensively studied and therefore, poorly understood. In this study, we aimed to explore biological sex as a variable influencing response to TBI using
Language	English
Publishing date	2020-06-19
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2564214-5
ISSN	1664-2295
ISSN	1664-2295
DOI	10.3389/fneur.2020.00511
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Editorial: Long-term toxicity and epigenetic effects of environmental exposures.

Ruden, Douglas M / Wang, Kai / Wang, Kangxu / Perera, Bambarendage P U / Lee Petroff, Rebekah

Frontiers in genetics

2022 Volume 13, Page(s) 1044589

Language	English
Publishing date	2022-09-30
Publishing country	Switzerland
Document type	Editorial
ZDB-ID	2606823-0
ISSN	1664-8021
ISSN	1664-8021
DOI	10.3389/fgene.2022.1044589
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Article: A single cell transcriptomic fingerprint of stressed premature, imbalanced differentiation of embryonic stem cells.

Ruden, Ximena / Singh, Aditi / Marben, Teya / Tang, Wen / Awonuga, Awoniyi / Ruden, Douglas M / Puscheck, Elizabeth / Feng, Hao / Rappolee, Daniel

bioRxiv : the preprint server for biology

2023

Abstract: Cultured naïve pluripotent ESC differentiate into first lineage, XEN or second lineage, formative pluripotency. Hyperosmotic stress (sorbitol), like retinoic acid, decreases naive pluripotency and increases XEN in two ESC lines, as reported by bulk and ... ...

Abstract	Cultured naïve pluripotent ESC differentiate into first lineage, XEN or second lineage, formative pluripotency. Hyperosmotic stress (sorbitol), like retinoic acid, decreases naive pluripotency and increases XEN in two ESC lines, as reported by bulk and scRNAseq, analyzed by UMAP. Sorbitol overrides pluripotency in two ESC lines as reported by bulk and scRNAseq, analyzed by UMAP. UMAP analyzed the effects of 5 stimuli - three stressed (200-300mM sorbitol with leukemia inhibitory factor +LIF) and two unstressed (+LIF, normal stemness-NS and -LIF, normal differentiation-ND). Sorbitol and RA decrease naive pluripotency and increase subpopulations of 2-cell embryo-like and XEN sub-lineages; primitive, parietal, and visceral endoderm (VE). Between the naïve pluripotency and primitive endoderm clusters is a stress-induced cluster with transient intermediate cells with higher LIF receptor signaling, with increased Stat3, Klf4, and Tbx3 expression. Sorbitol, like RA, also suppresses formative pluripotency, increasing lineage imbalance. Although bulk RNAseq and gene ontology group analyses suggest that stress induces head organizer and placental markers, scRNAseq reveals few cells. But VE and placental markers/cells were in adjacent clusters, like recent reports. UMAPs show that dose-dependent stress overrides stemness to force premature lineage imbalance. Hyperosmotic stress induces lineage imbalance, and other toxicological stresses, like drugs with RA, may cause lineage imbalance, resulting in miscarriages or birth defects.
Language	English
Publishing date	2023-05-24
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.23.541952
Database	MEDical Literature Analysis and Retrieval System OnLINE

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