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Dear Colleagues,

The rising global epidemic of obesity, cardiovascular disease and diabetes underscores the current challenge of characterizing the metabolically responsive epigenome. Recent studies investigating the molecular mechanisms linking fat and glucose metabolism with the epigenome highlight important regulatory determinants that underpin the expression of genes implicated in disease yet remain poorly understood. Epigenomes is now accepting submissions for a collection on "Epigenetic Mechanisms in Diabetes Research". This Topical Collection is edited by Professor Sam El-Osta from Monash University and will accept original research results and reviews, as well as special interest topics related to methods and resources of exceptional interest on topics related to metabolic regulation by epigenetic mechanisms in health and disease. You can find all the information related to the new Topical Collection at the following link: https://www.mdpi.com/journal/epigenomes/special_issues/diabetes.

We kindly invite you to submit your unpublished work to this Epigenomes Topical Collection, "Epigenetic Mechanisms in Diabetes Research".

I do hope you will join me in this Topical Collection.

Prof. Dr. Assam El-Osta
Collection Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the collection website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Epigenomes is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1500 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Published Papers (3 papers)

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17 pages, 984 KiB

Open AccessReview

Retrotransposons and Diabetes Mellitus

by Andromachi Katsanou, Charilaos Kostoulas, Evangelos Liberopoulos, Agathocles Tsatsoulis, Ioannis Georgiou and Stelios Tigas

Epigenomes 2024, 8(3), 35; https://doi.org/10.3390/epigenomes8030035 - 6 Sep 2024

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Abstract

Retrotransposons are invasive genetic elements, which replicate by copying and pasting themselves throughout the genome in a process called retrotransposition. The most abundant retrotransposons by number in the human genome are Alu and LINE-1 elements, which comprise approximately 40% of the human genome. The ability of retrotransposons to expand and colonize eukaryotic genomes has rendered them evolutionarily successful and is responsible for creating genetic alterations leading to significant impacts on their hosts. Previous research suggested that hypomethylation of Alu and LINE-1 elements is associated with global hypomethylation and genomic instability in several types of cancer and diseases, such as neurodegenerative diseases, obesity, osteoporosis, and diabetes mellitus (DM). With the advancement of sequencing technologies and computational tools, the study of the retrotransposon’s association with physiology and diseases is becoming a hot topic among researchers. Quantifying Alu and LINE-1 methylation is thought to serve as a surrogate measurement of global DNA methylation level. Although Alu and LINE-1 hypomethylation appears to serve as a cellular senescence biomarker promoting genomic instability, there is sparse information available regarding their potential functional and biological significance in DM. This review article summarizes the current knowledge on the involvement of the main epigenetic alterations in the methylation status of Alu and LINE-1 retrotransposons and their potential role as epigenetic markers of global DNA methylation in the pathogenesis of DM. Full article

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0 pages, 7041 KiB

Open AccessArticle

Exploring Transcriptional Regulation of Beta Cell SASP by Brd4-Associated Proteins and Cell Cycle Control Protein p21

by Jasmine Manji, Jasmine Pipella, Gabriel Brawerman and Peter J. Thompson

Epigenomes 2024, 8(1), 10; https://doi.org/10.3390/epigenomes8010010 - 6 Mar 2024

Viewed by 2259

Abstract

Type 1 diabetes (T1D) is a metabolic disease resulting from progressive autoimmune destruction of insulin-producing pancreatic beta cells. Although the majority of beta cells are lost in T1D, a small subset undergoes senescence, a stress response involving growth arrest, DNA damage response, and activation of a senescence-associated secretory phenotype (SASP). SASP in beta cells of the nonobese diabetic (NOD) mouse model of T1D and primary human islets is regulated at the level of transcription by bromodomain extra-terminal (BET) proteins, but the mechanisms remain unclear. To explore how SASP is transcriptionally regulated in beta cells, we used the NOD beta cell line NIT-1 to model beta cell SASP and identified binding partners of BET protein Brd4 and explored the role of the cyclin-dependent kinase inhibitor p21. Brd4 interacted with a variety of proteins in senescent NIT-1 cells including subunits of the Ino80 chromatin remodeling complex, which was expressed in beta cells during T1D progression in NOD mice and in human beta cells of control, autoantibody-positive, and T1D donors as determined from single-cell RNA-seq data. RNAi knockdown of p21 during senescence in NIT-1 cells did not significantly impact viability or SASP. Taken together, these results suggest that Brd4 interacts with several protein partners during senescence in NIT-1 cells, some of which may play roles in SASP gene activation and that p21 is dispensable for the SASP in this beta cell model. Full article

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Figure 1

Figure 1
Regulation of SASP by BET proteins and identification of Brd4-associated proteins during senescence in NIT-1 cells. (A) Luminex assays measuring the concentration of SASP factors Pai1 and Igfbp3 in the 24 h conditioned media collected from NIT-1 cells control (vehicle, DMSO), or senescent cells (0.25 µM etoposide treatment) at 11 days post-etoposide washout. Following drug washout, cells were treated once with vehicle or iBET-762 (5 µM) until harvest. (B) A repeated experiment as in (A) except for assaying Igfpb3 secretion by normalizing the amount in the conditioned media to the viable cell counts at the end of the assay at day 7 post-etoposide washout. (C) Immunoprecipitation (IP) of Brd4 followed by Western blots for Brd4 and p53 from 100 µg of nuclear extract protein of control or senescent NIT-1 cells at day 6 post-etoposide treatment. Input is 3, 5, and 10 µg of nuclear extract and rabbit IgG was the species matched control IP. (D) Mass spectrometry was performed on IgG control and Brd4 IPs from senescent NIT-1 cell nuclear extracts in two independent experiments on senescent NIT-1 cells at day 6 post-etoposide treatment. The number of proteins identified uniquely or in common in the datasets are shown. Brd4 IP experiment 1 and 2 identified a total of 24 common accessions (22 different proteins). (E) Table listing the 22 different proteins in the Brd4 IP1 and IP2. Brd4 is highlighted in red, subunits of the Ino80 complex are in blue, and the Mediator complex is in green. ns, not significant, * p < 0.05, ** p < 0.005, one-way ANOVA. Full article ">Figure 2
Characterization of Ino80 protein and INO80 gene expression during T1D in NOD mice and humans, respectively. (A) Western blot analysis validating Ino80 antibody on a recombinant GST-tagged partial Ino80 protein (~90 kDa in size) with 200, 100, 50, 25 ng loaded per lane. (B) Western blot of Ino80 on 10 or 20 µg of nuclear extracts from human 293T cells as a control, or control and senescent NIT-1 cells at day 5 post-etoposide washout. Kap1 was a loading control. (C) Western blot of Ino80 on 10 µg of total RIPA protein extracts from 293T cells, C57BL6 3-month-old male testis and isolated islets from female NOD mice at indicated ages, including a 16-week-old diabetic NOD female. Beta-actin was a loading control. The 180 kDa and 130 kDa Ino80 bands from each sample were quantified relative to the beta-actin bands and plotted. (D) Immunohistochemistry and fluorescence staining of Ino80 along with insulin and DAPI as a nuclear counterstain on euglycemic NOD female mouse pancreas sections at 6 weeks, 14 weeks, and 17 weeks of age. Scale bars indicate 50 µm. (E) Analysis of publicly available single-cell RNA-seq data from PANC-DB (Human Pancreas Analysis Project) using CellxGene, comparing expression of INO80 with BRD4 across all beta cells in control donors (n = 27,160) or in autoantibody-positive (AA+) and T1D donors (n = 9238). Dots are colored according to BRD4 expression levels. Y-axis reports binned expression level of INO80 read-counts while the X-axis reports binned expression level of BRD4 read-counts. Full article ">Figure 3
RNAi knockdown of Cdkn1a during senescence in NIT-1 cells. (A,B) Viability (gated R3) and transfection efficiency (gated R5) histograms and quantifications of NIT-1 cells transfected with 25 nM siGLO-FITC or mock transfected, 24 h post-transfection. (C) qRT-PCR analysis of Cdkn1a or Ppia as a control gene in control or etoposide induced senescent NIT-1 cells (72 h post-etoposide treatment) at 24 h post-transfection with control non-targeting siRNA (siCtrl), or Cdkn1a siRNA. N = 3 or 4 biological replicates per KD, error bars are S.D. ns = not significant, ** p < 0.005, one-way ANOVAs. (D) Western blot analysis of p21 on whole cell protein extracts prepared from NIT-1 cells transfected with the indicated siRNAs at 24 h or 72 h post-transfection. Beta-actin was as a loading control. (E) Western blot analysis of p21 levels after transfection with control or Cdkn1a siRNA at 72 h post-transfection in control/non-senescent NIT-1 cells in n = 3 biological replicates per transfection. Vinculin was a loading control. Plot shows quantification of p21 normalized to vinculin, error bars are S.D. * p < 0.05 two-tailed t-test. (F) Upper plot: viability assay using trypan blue staining and automated cell counting (Bio-Rad TC-20) of control or senescent NIT-1 cells transfected with the indicated siRNAs at 24 h post-transfection. Data are n = 10–12 biological replicates (upper plot), error bars are S.D. Lower plot: viability assay as in upper plot except 48 h following a second transfection which was conducted 2 days after the first transfection in control or senescent NIT-1 cells. Data are n = 3 or 4 biological replicates, error bars are S.D. ns = not significant, ** p < 0.005, *** p < 0.0005, two-tailed T-tests with multiple comparisons corrections (C,E) or two-way ANOVA in (F). Full article ">Figure 4
SASP gene activation is unaffected by KD of Cdkn1a in NIT-1 cells Control or senescent NIT-1 cells were transfected with indicated siRNAs and harvested 24 h post-transfection for qRT-PCR analysis of SASP genes Igfbp3 and Serpine1 (encoding Pai1). Data are n = 3 or 4 biological replicates, error bars are S.D. ns = not significant, ** p < 0.005, **** p < 0.0001, two-way ANOVA. Full article ">

Abstract

Gestational diabetes mellitus (GDM) is a pregnancy complication first detected in the second or third trimester in women that did not show evident glucose intolerance or diabetes before gestation. In 2019, the International Diabetes Federation reported that 15.8% of live births were affected by hyperglycemia during pregnancy, of which 83.6% were due to gestational diabetes mellitus, 8.5% were due to diabetes first detected in pregnancy, and 7.9% were due to diabetes detected before pregnancy. GDM increases the susceptibility to developing chronic diseases for both the mother and the baby later in life. Under GDM conditions, the intrauterine environment becomes hyperglycemic, while also showing high concentrations of fatty acids and proinflammatory cytokines, producing morphological, structural, and molecular modifications in the placenta, affecting its function; these alterations may predispose the baby to disease in adult life. Molecular alterations include epigenetic mechanisms such as DNA and RNA methylation, chromatin remodeling, histone modifications, and expression of noncoding RNAs (ncRNAs). The placenta is a unique organ that originates only in pregnancy, and its main function is communication between the mother and the fetus, ensuring healthy development. Thus, this review provides up-to-date information regarding two of the best-documented (epigenetic) mechanisms (DNA methylation and miRNA expression) altered in the human placenta under GDM conditions, as well as potential implications for the offspring. Full article

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