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Maciel SVSA, Oliveira IPP, Senes BB, Silva JAIDV, Feitosa FLB, Alves JS, Costa RB, de Camargo GMF. Genomic regions associated with coat color in Gir cattle. Genome 2024; 67:233-242. [PMID: 38579337 DOI: 10.1139/gen-2023-0115] [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] [Indexed: 04/07/2024]
Abstract
Indicine cattle breeds are adapted to the tropical climate, and their coat plays an important role in this process. Coat color influences thermoregulation and the adhesion of ectoparasites and may be associated with productive and reproductive traits. Furthermore, coat color is used for breed qualification, with breeders preferring certain colors. The Gir cattle is characterized by a wide variety of coat colors. Therefore, we performed genome-wide association studies to identify candidate genes for coat color in Gir cattle. Different phenotype scenarios were considered in the analyses and regions were identified on eight chromosomes. Some regions and many candidate genes are influencing coat color in the Gir cattle, which was found to be a polygenic trait. The candidate genes identified have been associated with white spotting patterns and base coat color in cattle and other species. In addition, a possible epistatic effect on coat color determination in the Gir cattle was suggested. This is the first published study that identified genomic regions and listed candidate genes associated with coat color in Gir cattle. The findings provided a better understanding of the genetic architecture of the trait in the breed and will allow to guide future fine-mapping studies for the development of genetic markers for selection.
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Ye H, Soede NM, Kemp B, Wang J, Fleuren M, Laurenssen B, Bouwman E, Langendijk P. Lactation body condition loss impaired conceptus development and plasma progesterone concentration at day 8 post-ovulation in primiparous sows. Theriogenology 2024; 218:174-182. [PMID: 38330861 DOI: 10.1016/j.theriogenology.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
The current study investigated effects of dietary amino acid (AA) availability on lactational body condition loss and metabolic status, in relation to reproductive parameters after weaning up to Day 8 post-ovulation. Primiparous sows (n = 35) were allocated to one of two lactation diets containing either low crude protein (CP, 140 g/kg) with a low percentage (8%) of slow protein in total protein (LL, n = 18) or high CP (180 g/kg) with a high (16%) percentage of slow protein (HH, n = 17). The HH diet was expected to improve AA utilization by supplying more AA, in a more gradual fashion. The diets did not affect sow body condition loss during lactation, while the HH diet tended to increase litter weight gain during the week 3 of lactation (Δ = 1.3 kg, P = 0.09). On Day 14 post-farrowing, HH diet led to higher plasma urea both pre-feeding and post-feeding (Δ = 2.3 mmol/L, P < 0.01, Δ = 2.4 mmol/L, P < 0.01, respectively), whilst plasma creatinine, NEFA and IGF-1 were similar. No dietary effects on reproductive parameters were found, however several relationships were found between body condition and reproductive parameters. Sows with higher body weight on Day 1 or Day 21 post-farrowing had greater follicle size on Day 3 post-weaning (β = 0.03 mm/kg, P < 0.01, β = 0.04 mm/kg, P < 0.01, respectively). At Day 8 post-ovulation, plasma progesterone concentration was negatively related to loin muscle loss (β = -0.67 ng/ml · mm-1, P = 0.02), backfat loss (β = -2.33 ng/ml · mm-1, P = 0.02), and estimated body fat loss (β = -0.67 ng/ml · mm-1, P = 0.02). Both plasma progesterone and the number of corpora lutea were positively related to the energy balance during lactation (β = 0.03 ng/ml · ME MJ-1, P = 0.01, β = 0.01 CL/ME MJ, P = 0.02, respectively). The conceptus size at Day 8 post-ovulation was negatively related to body weight loss (β = -0.01 mm/kg, P = 0.01), estimated body fat loss (β = -0.02 mm/kg, P = 0.03) and estimated body protein loss (β = -0.06 mm/kg, P = 0.04), and was positively related to the energy balance during lactation (β = 5.2*10-4 mm/ME MJ, P = 0.01). In conclusion, body protein and fat losses during lactation reduced subsequent plasma progesterone concentration and conceptus development at Day 8 post-ovulation.
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Affiliation(s)
- Hao Ye
- Adaptation Physiology, Wageningen University and Research, Wageningen, P.O. Box 338, 6700, AH, the Netherlands; State key Laboratory of Animal Nutrition and Feeding, China Agricultural University, Beijing, 00193, China
| | - Nicoline M Soede
- Adaptation Physiology, Wageningen University and Research, Wageningen, P.O. Box 338, 6700, AH, the Netherlands.
| | - Bas Kemp
- Adaptation Physiology, Wageningen University and Research, Wageningen, P.O. Box 338, 6700, AH, the Netherlands
| | - Junjun Wang
- State key Laboratory of Animal Nutrition and Feeding, China Agricultural University, Beijing, 00193, China
| | - Marleen Fleuren
- Trouw Nutrition R&D, Stationsstraat, 773811, MH, Amersfoort, the Netherlands
| | - Bjorge Laurenssen
- Adaptation Physiology, Wageningen University and Research, Wageningen, P.O. Box 338, 6700, AH, the Netherlands
| | - Emmy Bouwman
- Trouw Nutrition R&D, Stationsstraat, 773811, MH, Amersfoort, the Netherlands
| | - Pieter Langendijk
- Adaptation Physiology, Wageningen University and Research, Wageningen, P.O. Box 338, 6700, AH, the Netherlands; Trouw Nutrition R&D, Stationsstraat, 773811, MH, Amersfoort, the Netherlands
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Jubelin C, Muñoz-Garcia J, Ollivier E, Cochonneau D, Vallette F, Heymann MF, Oliver L, Heymann D. Identification of MCM4 and PRKDC as new regulators of osteosarcoma cell dormancy based on 3D cell cultures. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119660. [PMID: 38216092 DOI: 10.1016/j.bbamcr.2024.119660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 12/15/2023] [Accepted: 01/03/2024] [Indexed: 01/14/2024]
Abstract
Dormancy is a potential way for tumors to develop drug resistance and escape treatment. However, the mechanisms involved in cancer dormancy remain poorly understood. This is mainly because there is no in vitro culture model making it possible to spontaneously induce dormancy. In this context, the present work proposes the use of three-dimensional (3D) spheroids developed from osteosarcoma cell lines as a relevant model for studying cancer dormancy. MNNG-HOS, SaOS-2, 143B, MG-63, U2OS and SJSA-1 cell lines were cultured in 3D using the Liquid Overlay Technique (LOT). Dormancy was studied by staining cancer cells with a lipophilic dye (DiD), and long-term DiD+ cells were considered as dormant cancer cells. The role of the extracellular matrix in inducing dormancy was investigated by embedding cells into methylcellulose or Geltrex™. Gene expression of DiD+ cells was assessed with a Nanostring™ approach and the role of the genes detected in dormancy was validated by a transient down-expression model using siRNA treatment. Proliferation was measured using fluorescence microscopy and the xCELLigence technology. We observed that MNNG-HOS, 143B and MG-G3 cell lines had a reduced proliferation rate in 3D compared to 2D. U2OS cells had an increased proliferation rate when they were cultured in Geltrex™ compared to other 3D culture methods. Using 3D cultures, a transcriptomic signature of dormancy was obtained and showed a decreased expression of 18 genes including ETV4, HELLS, ITGA6, MCM4, PRKDC, RAD21 and UBE2T. The treatment with siRNA targeting these genes showed that cancer cell proliferation was reduced when the expression of ETV4 and MCM4 were decreased, whereas proliferation was increased when the expression of RAD21 was decreased. 3D culture facilitates the maintenance of dormant cancer cells characterized by a reduced proliferation and less differential gene expression as compared to proliferative cells. Further studies of the genes involved has enabled us to envisage their role in regulating cell proliferation.
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Affiliation(s)
- Camille Jubelin
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France; Institut de Cancérologie de l'Ouest, Tumor Heterogeneity and Precision Medicine Lab., 44805 Saint-Herblain, France; Atlantic Bone Screen, 44800 Saint-Herblain, France
| | - Javier Muñoz-Garcia
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France; Institut de Cancérologie de l'Ouest, Tumor Heterogeneity and Precision Medicine Lab., 44805 Saint-Herblain, France
| | - Emilie Ollivier
- Institut de Cancérologie de l'Ouest, Tumor Heterogeneity and Precision Medicine Lab., 44805 Saint-Herblain, France
| | - Denis Cochonneau
- Institut de Cancérologie de l'Ouest, Tumor Heterogeneity and Precision Medicine Lab., 44805 Saint-Herblain, France
| | - François Vallette
- Institut de Cancérologie de l'Ouest, Tumor Heterogeneity and Precision Medicine Lab., 44805 Saint-Herblain, France; Nantes Université, INSERM, CRCI(2)NA, UMR1307, 44000 Nantes, France
| | - Marie-Françoise Heymann
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France; Institut de Cancérologie de l'Ouest, Tumor Heterogeneity and Precision Medicine Lab., 44805 Saint-Herblain, France
| | - Lisa Oliver
- Nantes Université, INSERM, CRCI(2)NA, UMR1307, 44000 Nantes, France; CHU de Nantes, Nantes, France
| | - Dominique Heymann
- Nantes Université, CNRS, US2B, UMR 6286, 44000 Nantes, France; Institut de Cancérologie de l'Ouest, Tumor Heterogeneity and Precision Medicine Lab., 44805 Saint-Herblain, France; Department of Oncology and Metabolism, Medical School, University of Sheffield, Sheffield, UK.
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Vukic M, Chouaref J, Della Chiara V, Dogan S, Ratner F, Hogenboom JZM, Epp TA, Chawengsaksophak K, Vonk KKD, Breukel C, Ariyurek Y, San Leon Granado D, Kloet SL, Daxinger L. CDCA7-associated global aberrant DNA hypomethylation translates to localized, tissue-specific transcriptional responses. SCIENCE ADVANCES 2024; 10:eadk3384. [PMID: 38335290 PMCID: PMC10857554 DOI: 10.1126/sciadv.adk3384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 01/09/2024] [Indexed: 02/12/2024]
Abstract
Disruption of cell division cycle associated 7 (CDCA7) has been linked to aberrant DNA hypomethylation, but the impact of DNA methylation loss on transcription has not been investigated. Here, we show that CDCA7 is critical for maintaining global DNA methylation levels across multiple tissues in vivo. A pathogenic Cdca7 missense variant leads to the formation of large, aberrantly hypomethylated domains overlapping with the B genomic compartment but without affecting the deposition of H3K9 trimethylation (H3K9me3). CDCA7-associated aberrant DNA hypomethylation translated to localized, tissue-specific transcriptional dysregulation that affected large gene clusters. In the brain, we identify CDCA7 as a transcriptional repressor and epigenetic regulator of clustered protocadherin isoform choice. Increased protocadherin isoform expression frequency is accompanied by DNA methylation loss, gain of H3K4 trimethylation (H3K4me3), and increased binding of the transcriptional regulator CCCTC-binding factor (CTCF). Overall, our in vivo work identifies a key role for CDCA7 in safeguarding tissue-specific expression of gene clusters via the DNA methylation pathway.
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Affiliation(s)
- Maja Vukic
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Jihed Chouaref
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Serkan Dogan
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Fallon Ratner
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Trevor A. Epp
- Laboratory of Cell Differentiation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
- CZ-OPENSCREEN, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kallayanee Chawengsaksophak
- Laboratory of Cell Differentiation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kelly K. D. Vonk
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Cor Breukel
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Yavuz Ariyurek
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Susan L. Kloet
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
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Du X, Zhang X, Qi Z, Zeng Z, Xu Y, Yu Z, Cao X, Xia J. HELLS modulates the stemness of intrahepatic cholangiocarcinoma through promoting senescence-associated secretory phenotype. Comput Struct Biotechnol J 2023; 21:5174-5185. [PMID: 37920816 PMCID: PMC10618119 DOI: 10.1016/j.csbj.2023.09.020] [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: 05/11/2023] [Revised: 09/17/2023] [Accepted: 09/17/2023] [Indexed: 11/04/2023] Open
Abstract
The senescence-associated secretory phenotype (SASP) is closely associated with the tumorigenesis and progression of intrahepatic cholangiocarcinoma (ICC). However, it remains unclear its relation to stemness of ICC. In the study, the stemness indices of ICC were calculated using one-class linear regression (OCLR) and single-sample gene set enrichment analysis (ssGSEA) algorithms. A total of 14 senescence-related stemness genes (SRSGs) were identified using Pearson correlation analysis in ICC. Subsequently, a SRSGs-related classification was established using a consensus clustering for ICC. Different types of ICC exhibit distinct prognosis, immunity, metabolisms, and oncogenic signatures. Additionally, we constructed a risk score model for ICC using principal component analysis (PCA). The risk score was positively correlated with stemness, immune infiltration, metabolisms and oncogenic signatures, but negatively with prognosis in ICC. Patients with a high risk score may respond well to immunotherapy. Furthermore, we employed 3D fibrin gels to select tumor-repopulating cells (TRC) with stemness features. We found that HELLS, belonging to the 14 SRSGs, was up-regulated in ICC-TRC. And silencing HELLS significantly reduced the colony size, inhibited migration and invasion, and attenuated SASP in ICC-TRC. In summary, we provided a novel classification and risk score for ICC and uncovered a molecular mechanism via which CSLCs could obtain an active SASP.
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Affiliation(s)
- Xiaojing Du
- Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Endoscopy Center, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xingxing Zhang
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Department of Gastroenterology, Shanghai University of Medicine & Health Sciences Affiliated Sixth People’s Hospital South Campus, Shanghai 201499, China
| | - Zhuoran Qi
- Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Department of Gastroenterology, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Ziyi Zeng
- Royal Prince Alfred Hospital, 50 Missenden Rd, Camperdown, NSW 2050, Australia
| | - Ye Xu
- Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Zhijie Yu
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
- Wenzhou Key Laboratory of Hematology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xin Cao
- Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Institute of Clinical Science, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Jinglin Xia
- Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
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Kirsch-Volders M, Fenech M. Towards prevention of aneuploidy-associated cellular senescence and aging: more questions than answers? MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2023; 792:108474. [PMID: 37866738 DOI: 10.1016/j.mrrev.2023.108474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 10/10/2023] [Accepted: 10/16/2023] [Indexed: 10/24/2023]
Abstract
The aim of this review is to discuss how aneuploidy contributes to the aging process, and to identify plausible strategies for its prevention. After an overview of mechanisms leading to aneuploidy and the major features of cellular senescence, we discuss the link between (i) aneuploidy and cellular senescence; (ii) aneuploidy and aging; and (iii) cellular senescence and aging. We also consider (i) interactions between aneuploidy, micronuclei, cellular senescence and aging, (ii) the potential of nutritional treatments to prevent aneuploidy-associated senescence and aging, and (iii) knowledge and technological gaps. Evidence for a causal link between aneuploidy, senescence and aging is emerging. In vitro, aneuploidy accompanies the entry into cellular senescence and can itself induce senescence. How aneuploidy contributes in vivo to cellular senescence is less clear. Several routes depending on aneuploidy and/or senescence converge towards chronic inflammation, the major driver of unhealthy aging. Aneuploidy can induce the pro-inflammatory Senescence Associated Secretory Phenotype (SASP), either directly or as a result of micronucleus (MN) induction leading to leakage of DNA into the cytoplasm and triggering of the cGAS-STING pathway of innate immune response. A major difficulty in understanding the impact of aneuploidy on senescence and aging in vivo, results from the heterogeneity of cellular senescence in different tissues at the cytological and molecular level. Due to this complexity, there is at the present time no biomarker or biomarker combination characteristic for all types of senescent cells. In conclusion, a deeper understanding of the critical role aneuploidy plays in cellular senescence and aging is essential to devise practical strategies to protect human populations from aneuploidy-associated pathologies. We discuss emerging evidence, based on in vitro and in vivo studies, that adequate amounts of specific micronutrients are essential for prevention of aneuploidy in humans and that precise nutritional intervention may be essential to help avoid the scourge of aneuploidy-driven diseases.
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Affiliation(s)
- Micheline Kirsch-Volders
- Laboratory for Cell Genetics, Department Biology, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
| | - Michael Fenech
- Clinical and Health Sciences, University of South Australia, SA 5000, Australia; Genome Health Foundation, North Brighton, SA 5048, Australia.
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Berger F, Muegge K, Richards EJ. Seminars in cell and development biology on histone variants remodelers of H2A variants associated with heterochromatin. Semin Cell Dev Biol 2023; 135:93-101. [PMID: 35249811 PMCID: PMC9440159 DOI: 10.1016/j.semcdb.2022.02.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/22/2022] [Accepted: 02/23/2022] [Indexed: 01/04/2023]
Abstract
Variants of the histone H2A occupy distinct locations in the genome. There is relatively little known about the mechanisms responsible for deposition of specific H2A variants. Notable exceptions are chromatin remodelers that control the dynamics of H2A.Z at promoters. Here we review the steps that identified the role of a specific class of chromatin remodelers, including LSH and DDM1 that deposit the variants macroH2A in mammals and H2A.W in plants, respectively. The function of these remodelers in heterochromatin is discussed together with their multiple roles in genome stability.
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Affiliation(s)
- Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| | - Kathrin Muegge
- Epigenetics Section, Frederick National Laboratory for Cancer Research in the Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA.
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Abstract
Changes in bone architecture and metabolism with aging increase the likelihood of osteoporosis and fracture. Age-onset osteoporosis is multifactorial, with contributory extrinsic and intrinsic factors including certain medical problems, specific prescription drugs, estrogen loss, secondary hyperparathyroidism, microenvironmental and cellular alterations in bone tissue, and mechanical unloading or immobilization. At the histological level, there are changes in trabecular and cortical bone as well as marrow cellularity, lineage switching of mesenchymal stem cells to an adipogenic fate, inadequate transduction of signals during skeletal loading, and predisposition toward senescent cell accumulation with production of a senescence-associated secretory phenotype. Cumulatively, these changes result in bone remodeling abnormalities that over time cause net bone loss typically seen in older adults. Age-related osteoporosis is a geriatric syndrome due to the multiple etiologies that converge upon the skeleton to produce the ultimate phenotypic changes that manifest as bone fragility. Bone tissue is dynamic but with tendencies toward poor osteoblastic bone formation and relative osteoclastic bone resorption with aging. Interactions with other aging physiologic systems, such as muscle, may also confer detrimental effects on the aging skeleton. Conversely, individuals who maintain their BMD experience a lower risk of fractures, disability, and mortality, suggesting that this phenotype may be a marker of successful aging. © 2023 American Physiological Society. Compr Physiol 13:4355-4386, 2023.
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Affiliation(s)
- Robert J Pignolo
- Department of Medicine, Divisions of Geriatric Medicine and Gerontology, Endocrinology, and Hospital Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA.,The Department of Physiology and Biomedical Engineering, and the Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, Minnesota, USA
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Prakash Yadav R, Leskinen S, Ma L, Mäkelä JA, Kotaja N. Chromatin remodelers HELLS, WDHD1 and BAZ1A are dynamically expressed during mouse spermatogenesis. Reproduction 2023; 165:49-63. [PMID: 36194437 PMCID: PMC9782464 DOI: 10.1530/rep-22-0240] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/04/2022] [Indexed: 11/09/2022]
Abstract
In brief Proper regulation of heterochromatin is critical for spermatogenesis. This study reveals the dynamic localization patterns of distinct chromatin regulators during spermatogenesis and disrupted sex chromatin status in spermatocytes in the absence of DICER. Abstract Heterochromatin is dynamically formed and organized in differentiating male germ cells, and its proper regulation is a prerequisite for normal spermatogenesis. While heterochromatin is generally transcriptionally silent, we have previously shown that major satellite repeat (MSR) DNA in the pericentric heterochromatin (PCH) is transcribed during spermatogenesis. We have also shown that DICER associates with PCH and is involved in the regulation of MSR-derived transcripts. To shed light on the heterochromatin regulation in the male germline, we studied the expression, localization and heterochromatin association of selected testis-enriched chromatin regulators in the mouse testis. Our results show that HELLS, WDHD1 and BAZ1A are dynamically expressed during spermatogenesis. They display limited overlap in expression, suggesting involvement in distinct heterochromatin-associated processes at different steps of differentiation. We also show that HELLS and BAZ1A interact with DICER and MSR chromatin. Interestingly, deletion of Dicer1 affects the sex chromosome heterochromatin status in late pachytene spermatocytes, as demonstrated by mislocalization of Polycomb protein family member SCML1 to the sex body. These data substantiate the importance of dynamic heterochromatin regulation during spermatogenesis and emphasize the key role of DICER in the maintenance of chromatin status in meiotic male germ cells.
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Affiliation(s)
- Ram Prakash Yadav
- 1Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Sini Leskinen
- 1Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Lin Ma
- 1Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Juho-Antti Mäkelä
- 1Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
| | - Noora Kotaja
- 1Institute of Biomedicine, Integrative Physiology and Pharmacology Unit, University of Turku, Turku, Finland
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The Chromatin Remodeler HELLS: A New Regulator in DNA Repair, Genome Maintenance, and Cancer. Int J Mol Sci 2022; 23:ijms23169313. [PMID: 36012581 PMCID: PMC9409174 DOI: 10.3390/ijms23169313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 02/06/2023] Open
Abstract
Robust, tightly regulated DNA repair is critical to maintaining genome stability and preventing cancer. Eukaryotic DNA is packaged into chromatin, which has a profound, yet incompletely understood, regulatory influence on DNA repair and genome stability. The chromatin remodeler HELLS (helicase, lymphoid specific) has emerged as an important epigenetic regulator of DNA repair, genome stability, and multiple cancer-associated pathways. HELLS belongs to a subfamily of the conserved SNF2 ATP-dependent chromatin-remodeling complexes, which use energy from ATP hydrolysis to alter nucleosome structure and packaging of chromatin during the processes of DNA replication, transcription, and repair. The mouse homologue, LSH (lymphoid-specific helicase), plays an important role in the maintenance of heterochromatin and genome-wide DNA methylation, and is crucial in embryonic development, gametogenesis, and maturation of the immune system. Human HELLS is abundantly expressed in highly proliferating cells of the lymphoid tissue, skin, germ cells, and embryonic stem cells. Mutations in HELLS cause the human immunodeficiency syndrome ICF (Immunodeficiency, Centromeric instability, Facial anomalies). HELLS has been implicated in many types of cancer, including retinoblastoma, colorectal cancer, hepatocellular carcinoma, and glioblastoma. Here, we review and summarize accumulating evidence highlighting important roles for HELLS in DNA repair, genome maintenance, and key pathways relevant to cancer development, progression, and treatment.
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Kohzaki M. Mammalian Resilience Revealed by a Comparison of Human Diseases and Mouse Models Associated With DNA Helicase Deficiencies. Front Mol Biosci 2022; 9:934042. [PMID: 36032672 PMCID: PMC9403131 DOI: 10.3389/fmolb.2022.934042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 12/01/2022] Open
Abstract
Maintaining genomic integrity is critical for sustaining individual animals and passing on the genome to subsequent generations. Several enzymes, such as DNA helicases and DNA polymerases, are involved in maintaining genomic integrity by unwinding and synthesizing the genome, respectively. Indeed, several human diseases that arise caused by deficiencies in these enzymes have long been known. In this review, the author presents the DNA helicases associated with human diseases discovered to date using recent analyses, including exome sequences. Since several mouse models that reflect these human diseases have been developed and reported, this study also summarizes the current knowledge regarding the outcomes of DNA helicase deficiencies in humans and mice and discusses possible mechanisms by which DNA helicases maintain genomic integrity in mammals. It also highlights specific diseases that demonstrate mammalian resilience, in which, despite the presence of genomic instability, patients and mouse models have lifespans comparable to those of the general population if they do not develop cancers; finally, this study discusses future directions for therapeutic applications in humans that can be explored using these mouse models.
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Kim MJ, Seong KY, Kim DS, Jeong JS, Kim SY, Lee S, Yang SY, An BS. Minoxidil-loaded hyaluronic acid dissolving microneedles to alleviate hair loss in an alopecia animal model. Acta Biomater 2022; 143:189-202. [PMID: 35202857 DOI: 10.1016/j.actbio.2022.02.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/09/2022] [Accepted: 02/10/2022] [Indexed: 12/18/2022]
Abstract
Alopecia is defined as hair loss in a part of the head due to various causes, such as drugs, stress and autoimmune disorders. Various therapeutic agents have been suggested depending on the cause of the condition and patient sex, and age. Minoxidil (MXD) is commonly used topically to treat alopecia, but its low absorption rate limits widespread use. To overcome the low absorption, we suggest microneedles (MNs) as controlled drug delivery systems that release MXD. We used hyaluronic acid (HA) to construct MN, as it is biocompatible and safe. We examined the effect of HA on the hair dermal papilla (HDP) cells that control the development of hair follicles. HA enhanced proliferation, migration, and aggregation of HDP cell by increasing cell-cell adhesion and decreasing cell substratum. These effects were mediated by the cluster of differentiation (CD)-44 and phosphorylation of serine‑threonine kinase (Akt). In chemotherapy-induced alopecia mice, topical application of HA tended to decrease chemotherapy-induced hair loss. Although the amount of MXD administered by HA-MNs was 10% of topical treatment, the MXD-containing HA-MNs (MXD-HA-MNs) showed better effects on the growth of hair than topical application of MXD. In summary, our results demonstrated that HA reduces hair loss in alopecia mice, and that delivery of MXD and HA using MXD-HA-MNs maximizes therapeutic effects and minimize the side effects of MXD for the treatment of alopecia. STATEMENT OF SIGNIFICANCE: (1) Significance, This work reports a new approach for treatment of alopecia using a dissolving microneedle (MN) prepared with hyaluronic acid (HA). The HA provided a better environment for cellular functions in the hair dermal papilla cells. The HA-MNs containing minoxidil (MXD) exhibited a significant reduction of hair loss, although amount of MXD contained in them was only 10% of topically applied MXD., (2) Scientific impact, This is the first report demonstrating the direct anti-alopecia effects of HA administrated in a transdermal route and the feasibility of novel therapeutics using MXD-containing HA-MNs. We believe that our work will excite interdisciplinary readers of Acta Biomaterialia, those who are interested in the natural polymers, drug delivery, and alopecia.
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13
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He C, Liu L. Hsa_circ_0072008 regulates cell proliferation, migration, and invasion in cervical squamous cell carcinoma via miR-1305/helicase, lymphoid specific (HELLS) axis. Bioengineered 2022; 13:8311-8322. [PMID: 35311456 PMCID: PMC9161871 DOI: 10.1080/21655979.2022.2048945] [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] [Indexed: 11/21/2022] Open
Abstract
Cervical squamous cell carcinoma (CESC) is one of the most common cancers in women. Recent studies have proved that circular RNAs (circRNAs) could regulate the progress of CESC, but the mechanism is still indistinct. In this work, we explored the roles of circ_0072008 in CESC. The expression levels of circ_0072008, microRNA-1305 (miR-1305) and mRNA of HELLS (helicase, lymphoid specific) were detected by quantitative real-time reverse transcription-polymerase chain reaction (qRT-PCR) in CESC tissues. Meanwhile, the level of HELLS was quantified by western blot analysis. Besides, the cell functions were examined by colony formation assay, 5-Ethynyl-2’-deoxyuridine (EdU) assay, wound healing assay, flow cytometry assay and western blot. Furthermore, the interaction between miR-1305 and circ_0072008 or HELLS was detected by dual-luciferase reporter assay. The function of circ_0072008 in CESC has also been further verified in vivo by xenograft model experiments. The levels of circ_0072008 and HELLS were upregulated, and the miR-1305 level was decreased in CESC tissues in contrast to that in normal tissues. For functional analysis, silencing circ_0072008 inhibited cell proliferation and cell migration, whereas enhanced cell apoptosis in CESC cells. In mechanism, circ_0072008 acted as a miR-1305 sponge to regulate the level of HELLS. Moreover, miR-1305 was confirmed to repress the progression of CESC cells by suppressing HELLS. Meanwhile, knockdown of circ_0072008 inhibited CESC cells growth in vivo. In conclusion, circ_0072008 facilitated CESC cell proliferation, migration, and invasion through increasing HELLS expression by regulating miR-1305, which also offered an underlying targeted therapy for CESC treatment.
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Affiliation(s)
- Chunhua He
- Department of Gynecology, Jingmen NO. 1 People's Hospital, Jingmen, Hubei, China
| | - Leng Liu
- Department of Gynecology, Jingmen NO. 1 People's Hospital, Jingmen, Hubei, China
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14
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Reinitz F, Chen EY, Nicolis di Robilant B, Chuluun B, Antony J, Jones RC, Gubbi N, Lee K, Ho WHD, Kolluru SS, Qian D, Adorno M, Piltti K, Anderson A, Monje M, Heller HC, Quake SR, Clarke MF. Inhibiting USP16 rescues stem cell aging and memory in an Alzheimer's model. eLife 2022; 11:66037. [PMID: 35311644 PMCID: PMC9122497 DOI: 10.7554/elife.66037] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/17/2022] [Indexed: 11/23/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disease observed with aging that represents the most common form of dementia. To date, therapies targeting end-stage disease plaques, tangles, or inflammation have limited efficacy. Therefore, we set out to identify a potential earlier targetable phenotype. Utilizing a mouse model of AD and human fetal cells harboring mutant amyloid precursor protein, we show cell intrinsic neural precursor cell (NPC) dysfunction precedes widespread inflammation and amyloid plaque pathology, making it the earliest defect in the evolution of the disease. We demonstrate that reversing impaired NPC self-renewal via genetic reduction of USP16, a histone modifier and critical physiological antagonist of the Polycomb Repressor Complex 1, can prevent downstream cognitive defects and decrease astrogliosis in vivo. Reduction of USP16 led to decreased expression of senescence gene Cdkn2a and mitigated aberrant regulation of the Bone Morphogenetic Signaling (BMP) pathway, a previously unknown function of USP16. Thus, we reveal USP16 as a novel target in an AD model that can both ameliorate the NPC defect and rescue memory and learning through its regulation of both Cdkn2a and BMP signaling.
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Affiliation(s)
- Felicia Reinitz
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Elizabeth Y Chen
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Benedetta Nicolis di Robilant
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | | | - Jane Antony
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Robert C Jones
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Neha Gubbi
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Karen Lee
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - William Hai Dang Ho
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Sai Saroja Kolluru
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Dalong Qian
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Maddalena Adorno
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - Katja Piltti
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, United States
| | - Aileen Anderson
- Sue and Bill Gross Stem Cell Research Center, University of California, Irvine, Irvine, United States
| | - Michelle Monje
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
| | - H Craig Heller
- Department of Biology, Stanford University, Stanford, United States
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, Stanford, United States
| | - Michael F Clarke
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, United States
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15
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Bamberger C, Pankow S, Yates JR. SMG1 and CDK12 Link ΔNp63α Phosphorylation to RNA Surveillance in Keratinocytes. J Proteome Res 2021; 20:5347-5358. [PMID: 34761935 PMCID: PMC10653645 DOI: 10.1021/acs.jproteome.1c00427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The tumor suppressor p53-like protein p63 is required for self-renewal of epidermal tissues. Loss of p63 or exposure to ultraviolet (UV) irradiation triggers terminal differentiation in keratinocytes. However, it remains unclear how p63 diverts epidermal cells from proliferation to terminal differentiation, thereby contributing to successful tissue self-renewal. Here, we used bottom-up proteomics to identify the proteome at the chromatin in normal human epidermal keratinocytes following UV irradiation and p63 depletion. We found that loss of p63 increased DNA damage and that UV irradiation recruited the cyclin-dependent kinase CDK12 and the serine/threonine protein kinase SMG1 to chromatin only in the presence of p63. A post-translational modification analysis of ΔNp63α with mass spectrometry revealed that phosphorylation of T357/S358 and S368 was dependent on SMG1, whereas CDK12 increased the phosphorylation of ΔNp63α at S66/S68 and S301. Indirect phosphorylation of ΔNp63α in the presence of SMG1 enabled ΔNp63α to bind to the tumor suppressor p53-specific DNA recognition sequence, whereas CDK12 rendered ΔNp63α less responsive to UV irradiation and was not required for specific DNA binding. CDK12 and SMG1 are known to regulate the transcription and splicing of RNAs and the decay of nonsense RNAs, respectively, and a subset of p63-specific protein-protein interactions at the chromatin also linked p63 to RNA transcription and decay. We observed that in the absence of p63, UV irradiation resulted in more ORF1p. ORF1p is the first protein product of the intronless non-LTR retrotransposon LINE-1, indicating a derailed surveillance of RNA processing and/or translation. Our results suggest that p63 phosphorylation and transcriptional activation might correspond to altered RNA processing and/or translation to protect proliferating keratinocytes from increased genotoxic stress.
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Affiliation(s)
- Casimir Bamberger
- Department for Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Sandra Pankow
- Department for Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - John R. Yates
- Department for Chemical Physiology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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16
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Long J, Liu J, Xia A, Springer NM, He Y. Maize decrease in DNA methylation 1 targets RNA-directed DNA methylation on active chromatin. THE PLANT CELL 2021; 33:2183-2196. [PMID: 33779761 PMCID: PMC8364229 DOI: 10.1093/plcell/koab098] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 03/25/2021] [Indexed: 06/01/2023]
Abstract
DNA methylation plays vital roles in repressing transposable element activity and regulating gene expression. The chromatin-remodeling factor Decrease in DNA methylation 1 (DDM1) is crucial for maintaining DNA methylation across diverse plant species, and is required for RNA-directed DNA methylation (RdDM) to maintain mCHH islands in maize (Zea mays). However, the mechanisms by which DDM1 is involved in RdDM are not well understood. In this work, we used chromatin immunoprecipitation coupled with high-throughput sequencing to ascertain the genome-wide occupancy of ZmDDM1 in the maize genome. The results revealed that ZmDDM1 recognized an 8-bp-long GC-rich degenerate DNA sequence motif, which is enriched in transcription start sites and other euchromatic regions. Meanwhile, 24-nucleotide siRNAs and CHH methylation were delineated at the edge of ZmDDM1-occupied sites. ZmDDM1 co-purified with Argonaute 4 (ZmAGO4) proteins, providing further evidence that ZmDDM1 is a component of RdDM complexes in planta. Consistent with this, the vast majority of ZmDDM1-targeted regions co-localized with ZmAGO4-bound genomic sites. Overall, our results suggest a model that ZmDDM1 may be recruited to euchromatic regions via recognition of a GC-rich motif, thereby remodeling chromatin to provide access for RdDM activities in maize.
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Affiliation(s)
- Jincheng Long
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Jinghan Liu
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Aiai Xia
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
| | - Nathan M. Springer
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN 55108, USA
| | - Yan He
- MOE Key Laboratory of Crop Heterosis and Utilization, National Maize Improvement Center of China, China Agricultural University, Beijing 100094, China
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17
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De Dieuleveult M, Bizet M, Colin L, Calonne E, Bachman M, Li C, Stancheva I, Miotto B, Fuks F, Deplus R. The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome. Epigenetics 2021; 17:422-443. [PMID: 33960278 DOI: 10.1080/15592294.2021.1917152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ten-Eleven Translocation (TET) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) leading to a dynamic epigenetic state of DNA that can influence transcription and chromatin organization. While TET proteins interact with complexes involved in transcriptional repression and activation, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene expression still remains limited. Here, we show that TET proteins interact with the chromatin remodelling protein lymphoid-specific helicase (LSH/HELLS) in vivo and in vitro. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESCs) knock out of Lsh leads to a significant reduction of 5-hydroxymethylation amount in the DNA. Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh, some regions of the genome gain 5hmC while others lose it, with mild correlation with gene expression changes. We further show that differentially hydroxymethylated regions did not completely overlap with differentially methylated regions indicating that changes in 5hmC distribution upon Lsh knock-out are not a direct consequence of 5mC decrease. Altogether, our results suggest that LSH, which interacts with TET proteins, contributes to the regulation of 5hmC levels and distribution in MEFs and ESCs.
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Affiliation(s)
- Maud De Dieuleveult
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium.,Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Laurence Colin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Martin Bachman
- Medicines Discovery Catapult, Alderley Park, Macclesfield, UK
| | - Chao Li
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Irina Stancheva
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Benoit Miotto
- Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
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18
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Huang D, Li Q, Sun X, Sun X, Tang Y, Qu Y, Liu D, Yu T, Li G, Tong T, Zhang Y. CRL4 DCAF8 dependent opposing stability control over the chromatin remodeler LSH orchestrates epigenetic dynamics in ferroptosis. Cell Death Differ 2021; 28:1593-1609. [PMID: 33288900 PMCID: PMC8166945 DOI: 10.1038/s41418-020-00689-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 11/06/2020] [Accepted: 11/16/2020] [Indexed: 01/28/2023] Open
Abstract
Despite the emerging evidence on ferroptosis implicated in diverse pathologies, molecular linkage between oxidative inducers and chromatin as epigenetic memory carrier for its propagation remains elusive. Here, we report the identification of two WD40 proteins DCAF8 and WDR76 as substrate adapter and molecular inhibitor respectively of the Cullin-4 RING ubiquitin ligase (CRL4) system for stability control of chromatin remodeler LSH. Degradation analysis and CRL4-DCAF8 complex reconstitution demonstrate that CRL4DCAF8 is a bona fide E3 ligase for LSH. In contrast, WDR76 antagonizes DCAF8-targeted LSH proteolysis through competitive inhibition of the holo-CRL4DCAF8-LSH complex assembly. Importantly, this opposing regulatory strategy is utilized in lipid hydroperoxide induced ferroptosis, where we identify key redox homeostasis genes significantly regulated by the DCAF8/WDR76/LSH axis through transcriptomic epistasis analysis. This regulation is mechanistically attributed to DNA hydroxymethylation fostered WDR76 interaction with LSH and increased ratio of DCAF8 to WDR76 for antagonistic LSH association accompanying decreased DNA oxidation along with ROS overproduction. Evaluation of epigenetic dynamics at ferroptosis gene promoters reveals linker histone H1- and LSH-associated transcriptional repression is coordinately removed upon lipid peroxidation stress. Together with the phenotypes driven by WDR76 and DCAF8 manipulations, these data identify DCAF8- and WDR76-adapted oxidative damage sensing through DNA hydroxymethylation for LSH degradation control as a crucial nexus in epigenetic regulation of ferroptosis.
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Affiliation(s)
- Daoyuan Huang
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Qian Li
- grid.11135.370000 0001 2256 9319Department of Orthodontics, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 100081 Beijing, China
| | - Xinpei Sun
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Xiwen Sun
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Yunyi Tang
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Yanan Qu
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Dawei Liu
- grid.11135.370000 0001 2256 9319Department of Orthodontics, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 100081 Beijing, China
| | - Tingting Yu
- grid.11135.370000 0001 2256 9319Department of Orthodontics, Peking University School and Hospital of Stomatology, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing Key Laboratory of Digital Stomatology, 100081 Beijing, China
| | - Guodong Li
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Tanjun Tong
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
| | - Yu Zhang
- grid.11135.370000 0001 2256 9319Peking University Research Center on Aging, Department of Biochemistry and Molecular Biology, Peking University Health Science Center, 100191 Beijing, China
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19
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Abstract
Malignancies of the erythroid lineage are rare but aggressive diseases. Notably, the first insights into their biology emerged over half a century ago from avian and murine tumor viruses-induced erythroleukemia models providing the rationale for several transgenic mouse models that unraveled the transforming potential of signaling effectors and transcription factors in the erythroid lineage. More recently, genetic roadmaps have fueled efforts to establish models that are based on the epigenomic lesions observed in patients with erythroid malignancies. These models, together with often unexpected erythroid phenotypes in genetically modified mice, provided further insights into the molecular mechanisms of disease initiation and maintenance. Here, we review how the increasing knowledge of human erythroleukemia genetics combined with those from various mouse models indicate that the pathogenesis of the disease is based on the interplay between signaling mutations, impaired TP53 function, and altered chromatin organization. These alterations lead to aberrant activity of erythroid transcriptional master regulators like GATA1, indicating that erythroleukemia will most likely require combinatorial targeting for efficient therapeutic interventions.
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20
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Abstract
Age is a common risk factor in many diseases, but the molecular basis for this relationship is elusive. In this study we identified 4 disease clusters from 116 diseases in the UK Biobank data, defined by their age-of-onset profiles, and found that diseases with the same onset profile are genetically more similar, suggesting a common etiology. This similarity was not explained by disease categories, co-occurrences or disease cause-effect relationships. Two of the four disease clusters had an increased risk of occurrence from age 20 and 40 years respectively. They both showed an association with known aging-related genes, yet differed in functional enrichment and evolutionary profiles. Moreover, they both had age-related expression and methylation changes. We also tested mutation accumulation and antagonistic pleiotropy theories of aging and found support for both.
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21
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LSH mediates gene repression through macroH2A deposition. Nat Commun 2020; 11:5647. [PMID: 33159050 PMCID: PMC7648012 DOI: 10.1038/s41467-020-19159-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 09/22/2020] [Indexed: 02/07/2023] Open
Abstract
The human Immunodeficiency Centromeric Instability Facial Anomalies (ICF) 4 syndrome is a severe disease with increased mortality caused by mutation in the LSH gene. Although LSH belongs to a family of chromatin remodeling proteins, it remains unknown how LSH mediates its function on chromatin in vivo. Here, we use chemical-induced proximity to rapidly recruit LSH to an engineered locus and find that LSH specifically induces macroH2A1.2 and macroH2A2 deposition in an ATP-dependent manner. Tethering of LSH induces transcriptional repression and silencing is dependent on macroH2A deposition. Loss of LSH decreases macroH2A enrichment at repeat sequences and results in transcriptional reactivation. Likewise, reduction of macroH2A by siRNA interference mimicks transcriptional reactivation. ChIP-seq analysis confirmed that LSH is a major regulator of genome-wide macroH2A distribution. Tethering of ICF4 mutations fails to induce macroH2A deposition and ICF4 patient cells display reduced macroH2A deposition and transcriptional reactivation supporting a pathogenic role for altered marcoH2A deposition. We propose that LSH is a major chromatin modulator of the histone variant macroH2A and that its ability to insert marcoH2A into chromatin and transcriptionally silence is disturbed in the ICF4 syndrome. The human ICF 4 syndrome is caused by mutation of the chromatin remodeller LSH. Here, the authors show that LSH depletion disrupts the ability of histone variant macroH2A to insert into chromatin and silence transcription.
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22
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Liu N, Yang R, Shi Y, Chen L, Liu Y, Wang Z, Liu S, Ouyang L, Wang H, Lai W, Mao C, Wang M, Cheng Y, Liu S, Wang X, Zhou H, Cao Y, Xiao D, Tao Y. The cross-talk between methylation and phosphorylation in lymphoid-specific helicase drives cancer stem-like properties. Signal Transduct Target Ther 2020; 5:197. [PMID: 32994405 PMCID: PMC7524730 DOI: 10.1038/s41392-020-00249-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 06/20/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022] Open
Abstract
Posttranslational modifications (PTMs) of proteins, including chromatin modifiers, play crucial roles in the dynamic alteration of various protein properties and functions including stem-cell properties. However, the roles of Lymphoid-specific helicase (LSH), a DNA methylation modifier, in modulating stem-like properties in cancer are still not clearly clarified. Therefore, exploring PTMs modulation of LSH activity will be of great significance to further understand the function and activity of LSH. Here, we demonstrate that LSH is capable to undergo PTMs, including methylation and phosphorylation. The arginine methyltransferase PRMT5 can methylate LSH at R309 residue, meanwhile, LSH could as well be phosphorylated by MAPK1 kinase at S503 residue. We further show that the accumulation of phosphorylation of LSH at S503 site exhibits downregulation of LSH methylation at R309 residue, which eventually promoting stem-like properties in lung cancer. Whereas, phosphorylation-deficient LSH S503A mutant promotes the accumulation of LSH methylation at R309 residue and attenuates stem-like properties, indicating the critical roles of LSH PTMs in modulating stem-like properties. Thus, our study highlights the importance of the crosstalk between LSH PTMs in determining its activity and function in lung cancer stem-cell maintenance.
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Affiliation(s)
- Na Liu
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China.,Postdoctoral Research Workstation, Department of Neurosurgery, Xiangya Hospital, Central South University, 410078, Hunan, China
| | - Rui Yang
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Ying Shi
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Ling Chen
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Yating Liu
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Zuli Wang
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Shouping Liu
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Lianlian Ouyang
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Haiyan Wang
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Weiwei Lai
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Chao Mao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Min Wang
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Yan Cheng
- Xiangya School of Pharmaceutical Sciences, Central South University, 410078, Changsha, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, 410008, Changsha, Hunan, China
| | - Xiang Wang
- Hunan Key Laboratory of Tumor Models and Individualized Medicine; Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, 410011, Changsha, China
| | - Hu Zhou
- Shanghai Institute of Material Medical, Chinese Academy of Sciences (CAS), 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, 201203, Shanghai, China
| | - Ya Cao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China
| | - Desheng Xiao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China.
| | - Yongguang Tao
- Department of Pathology, Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Xiangya Hospital; Central South University, 410078, Hunan, China. .,NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 410078, Changsha, Hunan, China. .,Hunan Key Laboratory of Tumor Models and Individualized Medicine; Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, 410011, Changsha, China.
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23
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Orellana CA, Martínez VS, MacDonald MA, Henry MN, Gillard M, Gray PP, Nielsen LK, Mahler S, Marcellin E. 'Omics driven discoveries of gene targets for apoptosis attenuation in CHO cells. Biotechnol Bioeng 2020; 118:481-490. [PMID: 32865815 DOI: 10.1002/bit.27548] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 07/22/2020] [Accepted: 08/14/2020] [Indexed: 12/15/2022]
Abstract
Chinese hamster ovary (CHO) cells are widely used in biopharmaceutical production. Improvements to cell lines and bioprocesses are constantly being explored. One of the major limitations of CHO cell culture is that the cells undergo apoptosis, leading to rapid cell death, which impedes reaching high recombinant protein titres. While several genetic engineering strategies have been successfully employed to reduce apoptosis, there is still room to further enhance CHO cell lines performance. 'Omics analysis is a powerful tool to better understand different phenotypes and for the identification of gene targets for engineering. Here, we present a comprehensive review of previous CHO 'omics studies that revealed changes in the expression of apoptosis-related genes. We highlight targets for genetic engineering that have reduced, or have the potential to reduce, apoptosis or to increase cell proliferation in CHO cells, with the final aim of increasing productivity.
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Affiliation(s)
- Camila A Orellana
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia.,Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Verónica S Martínez
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Michael A MacDonald
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Matthew N Henry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Marianne Gillard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Peter P Gray
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Lars K Nielsen
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia.,Metabolomics Australia, The University of Queensland, Brisbane, Australia.,The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Stephen Mahler
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia
| | - Esteban Marcellin
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Australia.,Metabolomics Australia, The University of Queensland, Brisbane, Australia
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24
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He Y, Ren J, Xu X, Ni K, Schwader A, Finney R, Wang C, Sun L, Klarmann K, Keller J, Tubbs A, Nussenzweig A, Muegge K. Lsh/HELLS is required for B lymphocyte development and immunoglobulin class switch recombination. Proc Natl Acad Sci U S A 2020; 117:20100-20108. [PMID: 32727902 PMCID: PMC7443918 DOI: 10.1073/pnas.2004112117] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mutation of HELLS (Helicase, Lymphoid-Specific)/Lsh in human DNA causes a severe immunodeficiency syndrome, but the nature of the defect remains unknown. We assessed here the role of Lsh in hematopoiesis using conditional Lsh knockout mice with expression of Mx1 or Vav Cre-recombinase. Bone marrow transplantation studies revealed that Lsh depletion in hematopoietic stem cells severely reduced B cell numbers and impaired B cell development in a hematopoietic cell-autonomous manner. Lsh-deficient mice without bone marrow transplantation exhibited lower Ig levels in vivo compared to controls despite normal peripheral B cell numbers. Purified B lymphocytes proliferated normally but produced less immunoglobulins in response to in vitro stimulation, indicating a reduced capacity to undergo class switch recombination (CSR). Analysis of germline transcripts, examination of double-stranded breaks using biotin-labeling DNA break assay, and End-seq analysis indicated that the initiation of the recombination process was unscathed. In contrast, digestion-circularization PCR analysis and high-throughput sequencing analyses of CSR junctions and a chromosomal break repair assay indicated an impaired ability of the canonical end-joining pathway in Lsh-deficient B cells. Our data suggest a hematopoietic cell-intrinsic role of Lsh in B cell development and in CSR providing a potential target for immunodeficiency therapy.
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Affiliation(s)
- Yafeng He
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Jianke Ren
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Xiaoping Xu
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Kai Ni
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Andrew Schwader
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Richard Finney
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892
| | - Can Wang
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Lei Sun
- Hematopoiesis and Stem Cell Biology Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
| | - Kimberly Klarmann
- Hematopoiesis and Stem Cell Biology Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
- Basic Science Program, Leidos Biomedical Research, Inc., Basic Science Program, Frederick National Laboratory, Frederick, MD 21702
| | - Jonathan Keller
- Hematopoiesis and Stem Cell Biology Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
- Basic Science Program, Leidos Biomedical Research, Inc., Basic Science Program, Frederick National Laboratory, Frederick, MD 21702
| | - Anthony Tubbs
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892
| | - Kathrin Muegge
- Epigenetics Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702;
- Hematopoiesis and Stem Cell Biology Section, Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702
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25
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Interaction of Deubiquitinase 2A-DUB/MYSM1 with DNA Repair and Replication Factors. Int J Mol Sci 2020; 21:ijms21113762. [PMID: 32466590 PMCID: PMC7312997 DOI: 10.3390/ijms21113762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 01/09/2023] Open
Abstract
The deubiquitination of histone H2A on lysine 119 by 2A-DUB/MYSM1, BAP1, USP16, and other enzymes is required for key cellular processes, including transcriptional activation, apoptosis, and cell cycle control, during normal hematopoiesis and tissue development, and in tumor cells. Based on our finding that MYSM1 colocalizes with γH2AX foci in human peripheral blood mononuclear cells, leukemia cells, and melanoma cells upon induction of DNA double-strand breaks with topoisomerase inhibitor etoposide, we applied a mass spectrometry-based proteomics approach to identify novel 2A-DUB/MYSM1 interaction partners in DNA-damage responses. Differential display of MYSM1 binding proteins significantly enriched after exposure of 293T cells to etoposide revealed an interacting network of proteins involved in DNA damage and replication, including factors associated with poor melanoma outcome. In the context of increased DNA-damage in a variety of cell types in Mysm1-deficient mice, in bone marrow cells upon aging and in UV-exposed Mysm1-deficient skin, our current mass spectrometry data provide additional evidence for an interaction between MYSM1 and key DNA replication and repair factors, and indicate a potential function of 2A-DUB/MYSM1 in DNA repair processes.
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26
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Zhu W, Li LL, Songyang Y, Shi Z, Li D. Identification and validation of HELLS (Helicase, Lymphoid-Specific) and ICAM1 (Intercellular adhesion molecule 1) as potential diagnostic biomarkers of lung cancer. PeerJ 2020; 8:e8731. [PMID: 32195055 PMCID: PMC7067188 DOI: 10.7717/peerj.8731] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/11/2020] [Indexed: 12/25/2022] Open
Abstract
Although lung cancer is one of the greatest threats to human health, its signaling pathway and related genes are still unknown. This study integrates data from three groups of people to study potential key candidate genes and pathways related to lung cancer. Expression profiles (GSE18842, GSE19188 and GSE27262), including 162 tumor tissue and 135 adjacent normal lung tissue samples, were integrated and analyzed. Differentially expressed genes (DEGs) and candidate genes were identified, their expression pathways were analyzed, and the diethylene glycol-related protein–protein interaction (PPI) network was analyzed. We identified 232 shared DEGs (40 upregulated and 192 down-regulated) from the three GSE datasets. The DEGs were clustered according to function and signaling pathway for significant enrichment analysis. In total, 129 nodes/DEGs were identified from the DEG PPI network complex. An improved prognosis was associated with increased Helicase, Lymphoid-Specific (HELLS) and decreased Intercellular adhesion molecule 1 (ICAM1) mRNA expression in lung cancer patients. In conclusion, we used integrated bioinformatics analysis to identify candidate genes and pathways in lung cancer to show that HELLS and ICAM1 might be the key genes related to tumorigenesis or tumor progression in lung cancer. Additional studies are needed to further explore the involved functional mechanisms.
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Affiliation(s)
- Wei Zhu
- Department of Occupational and Environmental Health, Wuhan University, School of Health Science, Wuhan, Hubei, China
| | - Lin Lin Li
- Department of Occupational and Environmental Health, Wuhan University, School of Health Science, Wuhan, Hubei, China
| | - Yiyan Songyang
- Department of Occupational and Environmental Health, Wuhan University, School of Health Science, Wuhan, Hubei, China
| | - Zhan Shi
- Human Biology Program, University of Toronto, Toronto, ON, Canada
| | - Dejia Li
- Department of Occupational and Environmental Health, Wuhan University, School of Health Science, Wuhan, Hubei, China
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27
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Kollárovič G, Topping CE, Shaw EP, Chambers AL. The human HELLS chromatin remodelling protein promotes end resection to facilitate homologous recombination and contributes to DSB repair within heterochromatin. Nucleic Acids Res 2020; 48:1872-1885. [PMID: 31802118 PMCID: PMC7038987 DOI: 10.1093/nar/gkz1146] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 11/18/2019] [Accepted: 11/22/2019] [Indexed: 11/23/2022] Open
Abstract
Efficient double-strand break repair in eukaryotes requires manipulation of chromatin structure. ATP-dependent chromatin remodelling enzymes facilitate different DNA repair pathways, during different stages of the cell cycle and in varied chromatin environments. The contribution of remodelling factors to double-strand break repair within heterochromatin during G2 is unclear. The human HELLS protein is a Snf2-like chromatin remodeller family member and is mutated or misregulated in several cancers and some cases of ICF syndrome. HELLS has been implicated in the DNA damage response, but its mechanistic function in repair is not well understood. We discover that HELLS facilitates homologous recombination at two-ended breaks and contributes to repair within heterochromatic regions during G2. HELLS promotes initiation of HR by facilitating end-resection and accumulation of CtIP at IR-induced foci. We identify an interaction between HELLS and CtIP and establish that the ATPase domain of HELLS is required to promote DSB repair. This function of HELLS in maintenance of genome stability is likely to contribute to its role in cancer biology and demonstrates that different chromatin remodelling activities are required for efficient repair in specific genomic contexts.
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Affiliation(s)
- Gabriel Kollárovič
- DNA-protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Caitríona E Topping
- DNA-protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Edward P Shaw
- DNA-protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Anna L Chambers
- DNA-protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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28
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Zocchi L, Mehta A, Wu SC, Wu J, Gu Y, Wang J, Suh S, Spitale RC, Benavente CA. Chromatin remodeling protein HELLS is critical for retinoblastoma tumor initiation and progression. Oncogenesis 2020; 9:25. [PMID: 32071286 PMCID: PMC7028996 DOI: 10.1038/s41389-020-0210-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 01/08/2023] Open
Abstract
Retinoblastoma is an aggressive childhood cancer of the developing retina that initiates by biallelic RB1 gene inactivation. Tumor progression in retinoblastoma is driven by epigenetics, as retinoblastoma genomes are stable, but the mechanism(s) that drive these epigenetic changes remain unknown. Lymphoid-specific helicase (HELLS) protein is an epigenetic modifier directly regulated by the RB/E2F pathway. In this study, we used novel genetically engineered mouse models to investigate the role of HELLS during retinal development and tumorigenesis. Our results indicate that Hells-null retinal progenitor cells divide, undergo cell-fate specification, and give rise to fully laminated retinae with minor bipolar cells defects, but normal retinal function. Despite the apparent nonessential role of HELLS in retinal development, failure to transcriptionally repress Hells during retinal terminal differentiation due to retinoblastoma (RB) family loss significantly contributes to retinal tumorigenesis. Loss of HELLS drastically reduced ectopic division of differentiating cells in Rb1/p107-null retinae, significantly decreased the incidence of retinoblastoma, delayed tumor progression, and increased overall survival. Despite its role in heterochromatin formation, we found no evidence that Hells loss directly affected chromatin accessibility in the retina but functioned as transcriptional co-activator of E2F3, decreasing expression of cell cycle genes. We propose that HELLS is a critical downstream mediator of E2F-dependent ectopic proliferation in RB-null retinae. Together with the nontoxic effect of HELLS loss in the developing retina, our results suggest that HELLS and its downstream pathways could serve as potential therapeutic targets for retinoblastoma.
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Affiliation(s)
- Loredana Zocchi
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Aditi Mehta
- Pediatric Hematology and Pediatric Oncology, Children's Hospital of Orange County, Orange, CA, 92868, USA.,Department of Graduate Medical Education, University of California, Irvine, CA, 92697, USA
| | - Stephanie C Wu
- Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA, 92697, USA.,Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, 92697, USA
| | - Yijun Gu
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA
| | - Jingtian Wang
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA
| | - Susie Suh
- Gavin Herbert Eye Institute, Department of Ophthalmology, University of California, Irvine, CA, 92697, USA
| | - Robert C Spitale
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA.,Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, 92697, USA
| | - Claudia A Benavente
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA. .,Department of Developmental and Cell Biology, University of California, Irvine, CA, 92697, USA. .,Chao Family Comprehensive Cancer Center, University of California, Irvine, CA, 92697, USA.
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29
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Rhinn M, Ritschka B, Keyes WM. Cellular senescence in development, regeneration and disease. Development 2019; 146:146/20/dev151837. [DOI: 10.1242/dev.151837] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
ABSTRACT
Cellular senescence is a state comprising an essentially irreversible proliferative arrest combined with phenotypic changes and pronounced secretory activity. Although senescence has long been linked with aging, recent studies have uncovered functional roles for senescence in embryonic development, regeneration and reprogramming, and have helped to advance our understanding of this process as a highly coordinated and programmed cellular state. In this Primer article, we summarize some of the key findings in the field and attempt to explain them in a simple model that reconciles the normal and pathological roles for senescence. We discuss how a primary role of cellular senescence is to contribute to normal development, cell plasticity and tissue repair, as a dynamic and tightly regulated cellular program. However, when this process is perturbed, the beneficial effects turn detrimental and can contribute to disease and aging.
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Affiliation(s)
- Muriel Rhinn
- Department of Development and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), Illkirch, France UMR7104
- Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France U1258
- Université de Strasbourg, Illkirch, France
| | - Birgit Ritschka
- Department of Development and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), Illkirch, France UMR7104
- Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France U1258
- Université de Strasbourg, Illkirch, France
| | - William M. Keyes
- Department of Development and Stem Cells, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 1 Rue Laurent Fries, 67404, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS), Illkirch, France UMR7104
- Institut National de la Santé et de la Recherche Médicale (INSERM), Illkirch, France U1258
- Université de Strasbourg, Illkirch, France
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30
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de Assis LVM, Moraes MN, Castrucci AMDL. The molecular clock in the skin, its functionality, and how it is disrupted in cutaneous melanoma: a new pharmacological target? Cell Mol Life Sci 2019; 76:3801-3826. [PMID: 31222374 PMCID: PMC11105295 DOI: 10.1007/s00018-019-03183-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/13/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023]
Abstract
The skin is the interface between the organism and the external environment, acting as its first barrier. Thus, this organ is constantly challenged by physical stimuli such as UV and infrared radiation, visible light, and temperature as well as chemicals and pathogens. To counteract the deleterious effects of the above-mentioned stimuli, the skin has complex defense mechanisms such as: immune and neuroendocrine systems; shedding of epidermal squamous layers and apoptosis of damaged cells; DNA repair; and pigmentary system. Here we have reviewed the current knowledge regarding which stimuli affect the molecular clock of the skin, the consequences to skin-related biological processes and, based on such knowledge, we suggest some therapeutic targets. We also explored the recent advances regarding the molecular clock disruption in melanoma, its impact on the carcinogenic process, and its therapeutic value in melanoma treatment.
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Affiliation(s)
- Leonardo Vinícius Monteiro de Assis
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, R. do Matão, Trav. 14, No. 101, São Paulo, 05508-090, Brazil
| | - Maria Nathalia Moraes
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, R. do Matão, Trav. 14, No. 101, São Paulo, 05508-090, Brazil
- School of Health Science, University Anhembi Morumbi, São Paulo, Brazil
| | - Ana Maria de Lauro Castrucci
- Laboratory of Comparative Physiology of Pigmentation, Department of Physiology, Institute of Biosciences, University of São Paulo, R. do Matão, Trav. 14, No. 101, São Paulo, 05508-090, Brazil.
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31
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Robinson MH, Maximov V, Lallani S, Farooq H, Taylor MD, Read RD, Kenney AM. Upregulation of the chromatin remodeler HELLS is mediated by YAP1 in Sonic Hedgehog Medulloblastoma. Sci Rep 2019; 9:13611. [PMID: 31541170 PMCID: PMC6754407 DOI: 10.1038/s41598-019-50088-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 08/22/2019] [Indexed: 12/29/2022] Open
Abstract
Medulloblastoma is a malignant pediatric tumor that arises from neural progenitors in the cerebellum. Despite a five-year survival rate of ~70%, nearly all patients incur adverse side effects from current treatment strategies that drastically impact quality of life. Roughly one-third of medulloblastoma are driven by aberrant activation of the Sonic Hedgehog (SHH) signaling pathway. However, the scarcity of genetic mutations in medulloblastoma has led to investigation of other mechanisms contributing to cancer pathogenicity including epigenetic regulation of gene expression. Here, we show that Helicase, Lymphoid Specific (HELLS), a chromatin remodeler with epigenetic functions including DNA methylation and histone modification, is induced by Sonic Hedgehog (SHH) in SHH-dependent cerebellar progenitor cells and the developing murine cerebella. HELLS is also up-regulated in mouse and human SHH medulloblastoma. Others have shown that HELLS activity generally results in a repressive chromatin state. Our results demonstrate that increased expression of HELLS in our experimental systems is regulated by the oncogenic transcriptional regulator YAP1 downstream of Smoothened, the positive transducer of SHH signaling. Elucidation of HELLS as one of the downstream effectors of the SHH pathway may lead to novel targets for precision therapeutics with the promise of better outcomes for SHH medulloblastoma patients.
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Affiliation(s)
- M Hope Robinson
- Department of Pediatric Oncology, Emory University, Atlanta, GA, 30322, USA
- Cancer Biology Graduate Program, Winship Cancer Institute, Emory University, Atlanta, GA, USA
| | - Victor Maximov
- Department of Pediatric Oncology, Emory University, Atlanta, GA, 30322, USA
| | - Shoeb Lallani
- Department of Pharmacology, Emory University, Atlanta, GA, 30322, USA
| | - Hamza Farooq
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Surgery, Department of Laboratory Medicine and Pathobiology, and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Michael D Taylor
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Division of Neurosurgery, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Surgery, Department of Laboratory Medicine and Pathobiology, and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Renee D Read
- Department of Pharmacology, Emory University, Atlanta, GA, 30322, USA
- Winship Cancer Institute, Atlanta, GA, 30322, USA
| | - Anna Marie Kenney
- Department of Pediatric Oncology, Emory University, Atlanta, GA, 30322, USA.
- Winship Cancer Institute, Atlanta, GA, 30322, USA.
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32
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Law CT, Wei L, Tsang FHC, Chan CYK, Xu IMJ, Lai RKH, Ho DWH, Lee JMF, Wong CCL, Ng IOL, Wong CM. HELLS Regulates Chromatin Remodeling and Epigenetic Silencing of Multiple Tumor Suppressor Genes in Human Hepatocellular Carcinoma. Hepatology 2019; 69:2013-2030. [PMID: 30516846 DOI: 10.1002/hep.30414] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/29/2018] [Indexed: 12/18/2022]
Abstract
Hepatocellular carcinoma (HCC) is the third most lethal cancer worldwide. Increasing evidence shows that epigenetic alterations play an important role in human carcinogenesis. Deregulation of DNA methylation and histone modifications have recently been characterized in HCC, but the significance of chromatin remodeling in liver carcinogenesis remains to be explored. In this study, by systematically analyzing the expression of chromatin remodeling genes in human HCCs, we found that helicase, lymphoid-specific (HELLS), an SWI2/SNF2 chromatin remodeling enzyme, was remarkably overexpressed in HCC. Overexpression of HELLS correlated with more aggressive clinicopathological features and poorer patient prognosis compared to patients with lower HELLS expression. We further showed that up-regulation of HELLS in HCC was conferred by hyperactivation of transcription factor specificity protein 1 (SP1). To investigate the functions of HELLS in HCC, we generated both gain-of-function and loss-of-function models by the CRISPR activation system, lentiviral short hairpin RNA, and the CRISPR/Cas9 genome editing system. We demonstrated that overexpression of HELLS augmented HCC cell proliferation and migration. In contrast, depletion of HELLS reduced HCC growth and metastasis both in vitro and in vivo. Moreover, inactivation of HELLS led to metabolic reprogramming and reversed the Warburg effect in HCC cells. Mechanistically, by integrating analysis of RNA sequencing and micrococcal nuclease sequencing, we revealed that overexpression of HELLS increased nucleosome occupancy, which obstructed the accessibility of enhancers and hindered formation of the nucleosome-free region (NFR) at the transcription start site. Though this mechanism, up-regulation of HELLS mediated epigenetic silencing of multiple tumor suppressor genes including E-cadherin, FBP1, IGFBP3, XAF1 and CREB3L3 in HCC. Conclusion: Our data reveal that HELLS is a key epigenetic driver of HCC; by altering the nucleosome occupancy at the NFR and enhancer, HELLS epigenetically suppresses multiple tumor suppressor genes to promote HCC progression.
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MESH Headings
- Animals
- Antigens, CD/metabolism
- Cadherins/metabolism
- Carcinoma, Hepatocellular/enzymology
- Carcinoma, Hepatocellular/etiology
- Cell Line, Tumor
- Chromatin Assembly and Disassembly
- DNA Helicases/genetics
- DNA Helicases/metabolism
- Epigenesis, Genetic
- Gene Expression Regulation, Neoplastic
- Genes, Tumor Suppressor
- Humans
- Liver Neoplasms, Experimental/enzymology
- Liver Neoplasms, Experimental/etiology
- Mice, Knockout
- Mice, Nude
- Neoplasm Metastasis
- Nucleosomes/metabolism
- Sp1 Transcription Factor/metabolism
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Affiliation(s)
- Cheuk-Ting Law
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Lai Wei
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
- The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
| | - Felice Ho-Ching Tsang
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
- The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
| | - Cerise Yuen-Ki Chan
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Iris Ming-Jing Xu
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Robin Kit-Ho Lai
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Daniel Wai-Hung Ho
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Joyce Man-Fong Lee
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Carmen Chak-Lui Wong
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Irene Oi-Lin Ng
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
| | - Chun-Ming Wong
- Department of Pathology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong
- State Key Laboratory of Liver Research, University of Hong Kong, Hong Kong
- The University of Hong Kong Shenzhen Institute of Research and Innovation, Shenzhen, China
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33
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Ren J, Finney R, Ni K, Cam M, Muegge K. The chromatin remodeling protein Lsh alters nucleosome occupancy at putative enhancers and modulates binding of lineage specific transcription factors. Epigenetics 2019; 14:277-293. [PMID: 30861354 PMCID: PMC6557562 DOI: 10.1080/15592294.2019.1582275] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 01/07/2019] [Accepted: 02/07/2019] [Indexed: 12/12/2022] Open
Abstract
Dynamic regulation of chromatin accessibility is a key feature of cellular differentiation during embryogenesis, but the precise factors that control access to chromatin remain largely unknown. Lsh/HELLS is critical for normal development and mutations of Lsh in human cause the ICF (Immune deficiency, Centromeric instability, Facial anomalies) syndrome, a severe immune disorder with multiple organ deficiencies. We report here that Lsh, previously known to regulate DNA methylation level, has a genome wide chromatin remodeling function. Using micrococcal nuclease (MNase)-seq analysis, we demonstrate that Lsh protects MNase accessibility at transcriptional regulatory regions characterized by DNase I hypersensitivity and certain histone 3 (H3) tail modifications associated with enhancers. Using an auxin-inducible degron system, allowing proteolytical degradation of Lsh, we show that Lsh mediated changes in nucleosome occupancy are independent of DNA methylation level and are characterized by reduced H3 occupancy. While Lsh mediated nucleosome occupancy prevents binding sites for transcription factors in wild type cells, depletion of Lsh leads to an increase in binding of ectopically expressed tissue specific transcription factors to their respective binding sites. Our data suggests that Lsh mediated chromatin remodeling can modulate nucleosome positioning at a subset of putative enhancers contributing to the preservation of cellular identity through regulation of accessibility.
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Affiliation(s)
- Jianke Ren
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
| | - Richard Finney
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kai Ni
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
| | - Maggie Cam
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, National Cancer Institute, Frederick, MD, USA
- Frederick National Laboratory for Cancer Research, Basic Science Program, Leidos Biomedical Research, Inc., Frederick, MD, USA
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34
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Pennings S, Revuelta A, McLaughlin KA, Abd Hadi NA, Petchreing P, Ottaviano R, Meehan RR. Dynamics and Mechanisms of DNA Methylation Reprogramming. EPIGENETICS AND REGENERATION 2019:19-45. [DOI: 10.1016/b978-0-12-814879-2.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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35
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A Reassessment of Genes Modulating Aging in Mice Using Demographic Measurements of the Rate of Aging. Genetics 2018; 208:1617-1630. [PMID: 29444805 PMCID: PMC5887152 DOI: 10.1534/genetics.118.300821] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/07/2018] [Indexed: 02/07/2023] Open
Abstract
Many studies have reported genetic interventions that have an effect on mouse life span; however, it is crucial to discriminate between manipulations of aging and aging-independent causes of life extension. Here, we used the Gompertz equation to determine whether previously reported aging-related mouse genes statistically affect the demographic rate of aging. Of 30 genetic manipulations previously reported to extend life span, for only two we found evidence of retarding demographic aging: Cisd2 and hMTH1. Of 24 genetic manipulations reported to shorten life span and induce premature aging features, we found evidence of five accelerating demographic aging: Casp2, Fn1, IKK-β, JunD, and Stub1. Overall, our reassessment found that only 15% of the genetic manipulations analyzed significantly affected the demographic rate of aging as predicted, suggesting that a relatively small proportion of interventions affecting longevity do so by regulating the rate of aging. By contrast, genetic manipulations affecting longevity tend to impact on aging-independent mortality. Our meta-analysis of multiple mouse longevity studies also reveals substantial variation in the controls used across experiments, suggesting that a short life span of controls is a potential source of bias. Overall, the present work leads to a reassessment of genes affecting the aging process in mice, with broad implications for our understanding of the genetics of mammalian aging and which genes may be more promising targets for drug discovery.
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36
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Ren J, Hathaway NA, Crabtree GR, Muegge K. Tethering of Lsh at the Oct4 locus promotes gene repression associated with epigenetic changes. Epigenetics 2018; 13:173-181. [PMID: 28621576 PMCID: PMC5873361 DOI: 10.1080/15592294.2017.1338234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/25/2017] [Accepted: 05/24/2017] [Indexed: 10/19/2022] Open
Abstract
Lsh is a chromatin remodeling factor that regulates DNA methylation and chromatin function in mammals. The dynamics of these chromatin changes and whether they are directly controlled by Lsh remain unclear. To understand the molecular mechanisms of Lsh chromatin controlled regulation of gene expression, we established a tethering system that recruits a Gal4-Lsh fusion protein to an engineered Oct4 locus through Gal4 binding sites in murine embryonic stem (ES) cells. We examined the molecular epigenetic events induced by Lsh binding including: histone modification, DNA methylation and chromatin accessibility to determine nucleosome occupancy before and after embryonic stem cell differentiation. Our results indicate that Lsh assists gene repression upon binding to the Oct4 promoter region. Furthermore, we detected less chromatin accessibility and reduced active histone modifications at the tethered site in undifferentiated ES, while GFP reporter gene expression and DNA methylation patterns remained unchanged at this stage. Upon differentiation, association of Lsh promotes transcriptional repression of the reporter gene accompanied by the increase of repressive histone marks and a gain of DNA methylation at distal and proximal Oct4 enhancer sites. Taken together, this approach allowed us to examine Lsh mediated epigenetic regulation as a dynamic process and revealed chromatin accessibility changes as the primary consequence of Lsh function.
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Affiliation(s)
- Jianke Ren
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Nathaniel A. Hathaway
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Gerald R. Crabtree
- Departments of Pathology and Developmental Biology, Stanford University School of Medicine, Howard Hughes Medical Institute, CA, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
- Basic Science Program, Leidos Biomedical Research, Inc., Mouse Cancer Genetics Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
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37
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Sultana Z, Maiti K, Dedman L, Smith R. Is there a role for placental senescence in the genesis of obstetric complications and fetal growth restriction? Am J Obstet Gynecol 2018; 218:S762-S773. [PMID: 29275823 DOI: 10.1016/j.ajog.2017.11.567] [Citation(s) in RCA: 84] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/23/2017] [Accepted: 11/08/2017] [Indexed: 12/11/2022]
Abstract
The placenta ages as pregnancy advances, yet its continued function is required for a successful pregnancy outcome. Placental aging is a physiological phenomenon; however, there are some placentas that show signs of aging earlier than others. Premature placental senescence and aging are implicated in a number of adverse pregnancy outcomes, including fetal growth restriction, preeclampsia, spontaneous preterm birth, and intrauterine fetal death. Here we discuss cellular senescence, a state of terminal proliferation arrest, and how senescence is regulated. We also explore the role of physiological placental senescence and how aberrant placental senescence alters placental function, contributing to the pathophysiology of fetal growth restriction, preeclampsia, spontaneous preterm labor/birth, and unexplained fetal death.
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38
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Sachse G, Church C, Stewart M, Cater H, Teboul L, Cox RD, Ashcroft FM. FTO demethylase activity is essential for normal bone growth and bone mineralization in mice. Biochim Biophys Acta Mol Basis Dis 2017; 1864:843-850. [PMID: 29203346 PMCID: PMC5798602 DOI: 10.1016/j.bbadis.2017.11.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 11/20/2017] [Accepted: 11/29/2017] [Indexed: 12/26/2022]
Abstract
The Fto gene locus has been linked to increased body weight
and obesity in human population studies, but the role of the actual FTO protein in
adiposity has remained controversial. Complete loss of FTO protein in mouse and of
FTO function in human patients has multiple and variable effects. To determine which
effects are due to the ability of FTO to demethylate mRNA, we genetically engineered
a mouse with a catalytically inactive form of FTO. Our results demonstrate that FTO
catalytic activity is not required for normal body composition although it is
required for normal body size and viability. Strikingly, it is also essential for
normal bone growth and mineralization, a previously unreported FTO
function. A mouse model for a human lethal FTO catalytic null
mutation was established. Lean/fat body composition and energy metabolism parameters
were unaffected. FTO catalytic activity was required for normal body size
and viability. Lack of FTO enzymatic activity caused substantial bone
demineralization.
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Affiliation(s)
- Gregor Sachse
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK.
| | - Chris Church
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK.
| | - Michelle Stewart
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK.
| | - Heather Cater
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK.
| | - Lydia Teboul
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK.
| | - Roger D Cox
- MRC Harwell Institute, Mammalian Genetics Unit and Mary Lyon Centre, Harwell Campus, Oxfordshire, OX11 0RD, UK.
| | - Frances M Ashcroft
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford OX1 3PT, UK.
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39
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D'Arcangelo D, Tinaburri L, Dellambra E. The Role of p16 INK4a Pathway in Human Epidermal Stem Cell Self-Renewal, Aging and Cancer. Int J Mol Sci 2017; 18:ijms18071591. [PMID: 28737694 PMCID: PMC5536078 DOI: 10.3390/ijms18071591] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 07/13/2017] [Accepted: 07/19/2017] [Indexed: 12/31/2022] Open
Abstract
The epidermis is a self-renewing tissue. The balance between proliferation and differentiation processes is tightly regulated to ensure the maintenance of the stem cell (SC) population in the epidermis during life. Aging and cancer may be considered related endpoints of accumulating damages within epidermal self-renewing compartment. p16INK4a is a potent inhibitor of the G1/S-phase transition of the cell cycle. p16INK4a governs the processes of SC self-renewal in several tissues and its deregulation may result in aging or tumor development. Keratinocytes are equipped with several epigenetic enzymes and transcription factors that shape the gene expression signatures of different epidermal layers and allow dynamic and coordinated expression changes to finely balance keratinocyte self-renewal and differentiation. These factors converge their activity in the basal layer to repress p16INK4a expression, protecting cells from senescence, and preserving epidermal homeostasis and regeneration. Several stress stimuli may activate p16INK4a expression that orchestrates cell cycle exit and senescence response. In the present review, we discuss the role of p16INK4a regulators in human epidermal SC self-renewal, aging and cancer.
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Affiliation(s)
- Daniela D'Arcangelo
- Laboratory of Vascular Pathology, Istituto Dermopatico dell'Immacolata, Istituto di Ricovero e Cura a Carattere Scientifico (IDI-IRCCS), Fondazione Luigi Maria Monti (FLMM), via Monti di Creta 104, 00167 Rome, Italy.
| | - Lavinia Tinaburri
- Molecular and Cell Biology Laboratory, Istituto Dermopatico dell'Immacolata, Istituto di Ricovero e Cura a Carattere Scientifico (IDI-IRCCS), Fondazione Luigi Maria Monti (FLMM), via Monti di Creta 104, 00167 Rome, Italy.
| | - Elena Dellambra
- Molecular and Cell Biology Laboratory, Istituto Dermopatico dell'Immacolata, Istituto di Ricovero e Cura a Carattere Scientifico (IDI-IRCCS), Fondazione Luigi Maria Monti (FLMM), via Monti di Creta 104, 00167 Rome, Italy.
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40
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Litwin I, Bakowski T, Maciaszczyk-Dziubinska E, Wysocki R. The LSH/HELLS homolog Irc5 contributes to cohesin association with chromatin in yeast. Nucleic Acids Res 2017; 45:6404-6416. [PMID: 28383696 PMCID: PMC5499779 DOI: 10.1093/nar/gkx240] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 03/28/2017] [Accepted: 04/03/2017] [Indexed: 11/29/2022] Open
Abstract
Accurate chromosome segregation is essential for every living cell as unequal distribution of chromosomes during cell division may result in genome instability that manifests in carcinogenesis and developmental disorders. Irc5 from Saccharomyces cerevisiae is a member of the conserved Snf2 family of ATP-dependent DNA translocases and its function is poorly understood. Here, we identify Irc5 as a novel interactor of the cohesin complex. Irc5 associates with Scc1 cohesin subunit and contributes to cohesin binding to chromatin. Disruption of IRC5 decreases cohesin levels at centromeres and chromosome arms, causing premature sister chromatid separation. Moreover, reduced cohesin occupancy at the rDNA region in cells lacking IRC5 leads to the loss of rDNA repeats. We also show that the translocase activity of Irc5 is required for its function in cohesion pathway. Finally, we demonstrate that in the absence of Irc5 both the level of chromatin-bound Scc2, a member of cohesin loading complex, and physical interaction between Scc1 and Scc2 are reduced. Our results suggest that Irc5 is an auxiliary factor that is involved in cohesin association with chromatin.
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Affiliation(s)
- Ireneusz Litwin
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland
| | - Tomasz Bakowski
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland
| | | | - Robert Wysocki
- Institute of Experimental Biology, University of Wroclaw, 50-328 Wroclaw, Poland
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41
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Han Y, Ren J, Lee E, Xu X, Yu W, Muegge K. Lsh/HELLS regulates self-renewal/proliferation of neural stem/progenitor cells. Sci Rep 2017; 7:1136. [PMID: 28442710 PMCID: PMC5430779 DOI: 10.1038/s41598-017-00804-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 03/16/2017] [Indexed: 12/11/2022] Open
Abstract
Epigenetic mechanisms are known to exert control over gene expression and determine cell fate. Genetic mutations in epigenetic regulators are responsible for several neurologic disorders. Mutations of the chromatin remodeling protein Lsh/HELLS can cause the human Immunodeficiency, Centromere instability and Facial anomalies (ICF) syndrome, which is associated with neurologic deficiencies. We report here a critical role for Lsh in murine neural development. Lsh depleted neural stem/progenitor cells (NSPCs) display reduced growth, increases in apoptosis and impaired ability of self-renewal. RNA-seq analysis demonstrates differential gene expression in Lsh-/- NSPCs and suggests multiple aberrant pathways. Concentrating on specific genomic targets, we show that ablation of Lsh alters epigenetic states at specific enhancer regions of the key cell cycle regulator Cdkn1a and the stem cell regulator Bmp4 in NSPCs and alters their expression. These results suggest that Lsh exerts epigenetic regulation at key regulators of neural stem cell fate ensuring adequate NSPCs self-renewal and maintenance during development.
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Affiliation(s)
- Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA
| | - Jianke Ren
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA
| | - Eunice Lee
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA
| | - Xiaoping Xu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA
| | - Weishi Yu
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA
| | - Kathrin Muegge
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, 21702, USA.
- Basic Science Program, Leidos Biomedical Research, Inc., Mouse Cancer Genetics Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 21702, USA.
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42
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Pauletto M, Milan M, Huvet A, Corporeau C, Suquet M, Planas JV, Moreira R, Figueras A, Novoa B, Patarnello T, Bargelloni L. Transcriptomic features of Pecten maximus oocyte quality and maturation. PLoS One 2017; 12:e0172805. [PMID: 28253290 PMCID: PMC5333834 DOI: 10.1371/journal.pone.0172805] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/09/2017] [Indexed: 11/19/2022] Open
Abstract
The king scallop Pecten maximus is a high valuable species of great interest in Europe for both fishery and aquaculture. Notably, there has been an increased investment to produce seed for enhancement programmes of wild scallop populations. However, hatchery production is a relatively new industry and it is still underdeveloped. Major hurdles are spawning control and gamete quality. In the present study, a total of 14 scallops were sampled in the bay of Brest (Brittany, France) to compare transcriptomic profiles of mature oocytes collected by spawning induction or by stripping. To reach such a goal, a microarray analysis was performed by using a custom 8x60K oligonucleotide microarray representing 45,488 unique scallop contigs. First we identified genes that were differentially expressed depending on oocyte quality, estimated as the potential to produce D-larvae. Secondly, we investigated the transcriptional features of both stripped and spawned oocytes. Genes coding for proteins involved in cytoskeletal dynamics, serine/threonine kinases signalling pathway, mRNA processing, response to DNA damage, apoptosis and cell-cycle appeared to be of crucial importance for both oocyte maturation and developmental competence. This study allowed us to dramatically increase the knowledge about transcriptional features of oocyte quality and maturation, as well as to propose for the first time putative molecular markers to solve a major bottleneck in scallop aquaculture.
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Affiliation(s)
- Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - Massimo Milan
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - Arnaud Huvet
- Ifremer, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des sciences de l’Environnement Marin (LEMAR), Plouzané, France
| | - Charlotte Corporeau
- Ifremer, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des sciences de l’Environnement Marin (LEMAR), Plouzané, France
| | - Marc Suquet
- Ifremer, UMR 6539 CNRS/UBO/IRD/Ifremer, Laboratoire des sciences de l’Environnement Marin (LEMAR), Plouzané, France
| | - Josep V. Planas
- Departament de Fisiologia i Immunologia, Facultat de Biologia, Universitat de Barcelona i Institut de Biomedicina de la Universitat de Barcelona, Barcelona, Spain
| | - Rebeca Moreira
- Instituto de Investigaciones Marinas (IIM-CSIC), Vigo, Pontevedra, Spain
| | - Antonio Figueras
- Instituto de Investigaciones Marinas (IIM-CSIC), Vigo, Pontevedra, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM-CSIC), Vigo, Pontevedra, Spain
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padova, Italy
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43
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Stenvinkel P, Luttropp K, McGuinness D, Witasp A, Rashid Qureshi A, Wernerson A, Nordfors L, Schalling M, Ripsweden J, Wennberg L, Söderberg M, Bárány P, Olauson H, Shiels PG. CDKN2A/p16INK4a expression is associated with vascular progeria in chronic kidney disease. Aging (Albany NY) 2017; 9:494-507. [PMID: 28192277 PMCID: PMC5361677 DOI: 10.18632/aging.101173] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2016] [Accepted: 02/03/2017] [Indexed: 04/08/2023]
Abstract
Patients with chronic kidney disease (CKD) display a progeric vascular phenotype linked to apoptosis, cellular senescence and osteogenic transformation. This has proven intractable to modelling appropriately in model organisms. We have therefore investigated this directly in man, using for the first time validated cellular biomarkers of ageing (CDKN2A/p16INK4a, SA-β-Gal) in arterial biopsies from 61 CKD patients undergoing living donor renal transplantation. We demonstrate that in the uremic milieu, increased arterial expression of CDKN2A/p16INK4a associated with vascular progeria in CKD, independently of chronological age. The arterial expression of CDKN2A/p16INK4a was significantly higher in patients with coronary calcification (p=0.01) and associated cardiovascular disease (CVD) (p=0.004). The correlation between CDKN2A/p16INK4a and media calcification was statistically significant (p=0.0003) after correction for chronological age. We further employed correlate expression of matrix Gla protein (MGP) and runt-related transcription factor 2 (RUNX2) as additional pathognomonic markers. Higher expression of CDKN2A/p16INK4a, RUNX2 and MGP were observed in arteries with severe media calcification. The number of p16INK4a and SA-β-Gal positive cells was higher in biopsies with severe media calcification. A strong inverse correlation was observed between CDKN2A/p16INK4a expression and carboxylated osteocalcin levels. Thus, impaired vitamin K mediated carboxylation may contribute to premature vascular senescence.
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Affiliation(s)
- Peter Stenvinkel
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Karin Luttropp
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Dagmara McGuinness
- Wolfson Wohl Translational Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Anna Witasp
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Abdul Rashid Qureshi
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Annika Wernerson
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Louise Nordfors
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Martin Schalling
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Jonaz Ripsweden
- Division of Radiology, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Stockholm, Sweden
| | - Lars Wennberg
- Division of Transplantation Surgery, Department of Clinical Science, Intervention and Technology, Karolinska University Hospital, Stockholm, Sweden
| | - Magnus Söderberg
- Pathology, Drug Safety and Metabolism, AstraZeneca, Mölndal, Sweden
| | - Peter Bárány
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Hannes Olauson
- Division of Renal Medicine, Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Stockholm, Sweden
| | - Paul G Shiels
- Wolfson Wohl Translational Research Centre, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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44
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Rani S, Bhardwaj S, Srivastava N, Sharma VL, Parsad D, Kumar R. Senescence in the lesional fibroblasts of non-segmental vitiligo patients. Arch Dermatol Res 2017; 309:123-132. [PMID: 28078437 DOI: 10.1007/s00403-016-1713-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/15/2016] [Accepted: 12/23/2016] [Indexed: 01/04/2023]
Abstract
Dermal fibroblasts secrete various growth factors which are important for skin pigmentation. Imbalance in the synchronization of epidermal and dermal cells in the skin can play vital role in the pathogenesis of pigmentary disorder vitiligo. Therefore, our objective was to check the lesional fibroblasts for any abnormality and senescence in non-segmental vitiligo patients (NSV). Skin punch biopsies were taken from NSV patients and healthy controls. Explant culture of fibroblast from lesional dermis, non-lesional dermis, and control was analyzed. The senescence was confirmed by β-galactosidase staining in the cultured fibroblasts. Senescence was checked at mRNA level in lesional dermis, non-lesional dermis of NSV patients by senescence markers p16, p21, and hp1 by quantitative real-time polymerase chain reaction (qRT-PCR) and immunofluorescence study was used for protein analysis. Morphological results showed number of fibroblasts with bigger perinuclear region and vacuoles were more in the lesional fibroblasts. Number of β-galactosidase positive fibroblasts in the lesional skin of NSV patients was higher as compared to the non-lesional and control fibroblasts. Results showed higher relative gene expression of senescence markers p16, p21, and hp1 in the lesional dermis of NSV patients at mRNA level and protein level as compared with control. Senescence in the dermal fibroblasts can decrease the secretion of growth factors and cytokines secreted by fibroblasts which may lead to the melanocyte death and progression of vitiligo. However, further studies on larger number of patients are needed to confirm the role of fibroblasts in the vitiligo pathogenesis.
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Affiliation(s)
- Seema Rani
- Department of Zoology, Panjab University, Chandigarh, 160014, India
| | - Supriya Bhardwaj
- Department of Dermatology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Niharika Srivastava
- Department of Dermatology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | | | - Davinder Parsad
- Department of Dermatology, Postgraduate Institute of Medical Education and Research, Chandigarh, 160012, India
| | - Ravinder Kumar
- Department of Zoology, Panjab University, Chandigarh, 160014, India.
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45
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Kobayashi N, Shinagawa S, Nagata T, Shimada K, Shibata N, Ohnuma T, Kasanuki K, Arai H, Yamada H, Nakayama K, Kondo K. Usefulness of DNA Methylation Levels in COASY and SPINT1 Gene Promoter Regions as Biomarkers in Diagnosis of Alzheimer's Disease and Amnestic Mild Cognitive Impairment. PLoS One 2016; 11:e0168816. [PMID: 27992572 PMCID: PMC5167410 DOI: 10.1371/journal.pone.0168816] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/06/2016] [Indexed: 12/31/2022] Open
Abstract
In order to conduct early therapeutic interventions for Alzheimer's disease (AD), convenient, early diagnosis markers are required. We previously reported that changes in DNA methylation levels were associated with amnestic mild cognitive impairment (aMCI) and AD. As the results suggested changes in DNA methylation levels in the COASY and SPINT1 gene promoter regions, in the present study we examined DNA methylation in these regions in normal controls (NCs, n = 30), aMCI subjects (n = 28) and AD subjects (n = 30) using methylation-sensitive high resolution melting (MS-HRM) analysis. The results indicated that DNA methylation in the two regions was significantly increased in AD and aMCI as compared to NCs (P < 0.0001, P < 0.0001, ANOVA). Further analysis suggested that DNA methylation in the COASY gene promoter region in particular could be a high sensitivity, high specificity diagnosis biomarker (COASY: sensitivity 96.6%, specificity 96.7%; SPINT1: sensitivity 63.8%, specificity 83.3%). DNA methylation in the COASY promoter region was associated with CDR Scale Sum of Boxes (CDR-SB), an indicator of dementia severity. In the SPINT1 promoter region, DNA methylation was negatively associated with age in NCs and elevated in aMCI and AD subjects positive for antibodies to Herpes simplex virus type 1 (HSV-1). These findings suggested that changes in DNA methylation in the COASY and SPINT1 promoter regions are influenced by various factors. In conclusion, DNA methylation levels in the COASY and SPINT1 promoter regions were considered to potentially be a convenient and useful biomarker for diagnosis of AD and aMCI.
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Affiliation(s)
- Nobuyuki Kobayashi
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan
| | | | - Tomoyuki Nagata
- Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan
- Division of Molecular Genetics, The Jikei University School of Medicine, Tokyo, Japan
| | - Kazuya Shimada
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan
| | - Nobuto Shibata
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Tohru Ohnuma
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Koji Kasanuki
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Heii Arai
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Hisashi Yamada
- Division of Molecular Genetics, The Jikei University School of Medicine, Tokyo, Japan
| | - Kazuhiko Nakayama
- Department of Psychiatry, The Jikei University School of Medicine, Tokyo, Japan
| | - Kazuhiro Kondo
- Department of Virology, The Jikei University School of Medicine, Tokyo, Japan
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46
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Rivera-Gonzalez GC, Shook BA, Andrae J, Holtrup B, Bollag K, Betsholtz C, Rodeheffer MS, Horsley V. Skin Adipocyte Stem Cell Self-Renewal Is Regulated by a PDGFA/AKT-Signaling Axis. Cell Stem Cell 2016; 19:738-751. [PMID: 27746098 DOI: 10.1016/j.stem.2016.09.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 07/14/2016] [Accepted: 09/11/2016] [Indexed: 12/15/2022]
Abstract
Tissue growth and maintenance requires stem cell populations that self-renew, proliferate, and differentiate. Maintenance of white adipose tissue (WAT) requires the proliferation and differentiation of adipocyte stem cells (ASCs) to form postmitotic, lipid-filled mature adipocytes. Here we use the dynamic adipogenic program that occurs during hair growth to uncover an unrecognized regulator of ASC self-renewal and proliferation, PDGFA, which activates AKT signaling to drive and maintain the adipogenic program in the skin. Pdgfa expression is reduced in aged ASCs and is required for ASC proliferation and maintenance in the dermis, but not in other WATs. Our molecular and genetic studies uncover PI3K/AKT2 as a direct PDGFA target that is activated in ASCs during WAT hyperplasia and is functionally required for dermal ASC proliferation. Our data therefore reveal active mechanisms that regulate ASC self-renewal in the skin and show that distinct regulatory mechanisms operate in different WAT depots.
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Affiliation(s)
| | - Brett A Shook
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Johanna Andrae
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Brandon Holtrup
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Katherine Bollag
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Christer Betsholtz
- Department of Immunology, Genetics and Pathology, Rudbeck Laboratory, Uppsala University, 751 85 Uppsala, Sweden
| | - Matthew S Rodeheffer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Section of Comparative Medicine, Yale University, New Haven, CT 06520, USA
| | - Valerie Horsley
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA; Department of Dermatology, Yale School of Medicine, Yale University, New Haven, CT 06520, USA.
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Devos M, Gilbert B, Denecker G, Leurs K, Mc Guire C, Lemeire K, Hochepied T, Vuylsteke M, Lambert J, Van Den Broecke C, Libbrecht L, Haigh J, Berx G, Lippens S, Vandenabeele P, Declercq W. Elevated ΔNp63α Levels Facilitate Epidermal and Biliary Oncogenic Transformation. J Invest Dermatol 2016; 137:494-505. [PMID: 27725202 DOI: 10.1016/j.jid.2016.09.026] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 09/05/2016] [Accepted: 09/20/2016] [Indexed: 12/23/2022]
Abstract
Unlike its family member p53, TP63 is rarely mutated in human cancer. However, ΔNp63α protein levels are often elevated in tumors of epithelial origin, such as squamous cell carcinoma and cholangiocarcinoma. To study the oncogenic properties of ΔNp63α in vivo, we generated transgenic mice overexpressing ΔNp63α from the Rosa26 locus promoter controlled by keratin 5-Cre. We found that these mice spontaneously develop epidermal cysts and ectopic ΔNp63α expression in the bile duct epithelium that leads to dilatation of the intrahepatic biliary ducts, to hepatic cyst formation and bile duct adenoma. Moreover, when subjected to models of 7,12-dimethylbenz[a]anthracene-based carcinogenesis, tumor initiation was increased in ΔNp63α transgenic mice in a gene dosage-dependent manner although ΔNp63α overexpression did not alter the sensitivity to 7,12-dimethylbenz[a]anthracene-induced cytotoxicity in vivo. However, keratinocytes isolated from ΔNp63α transgenic mice displayed increased survival and delayed cellular senescence compared with wild-type keratinocytes, marked by decreased p16Ink4a and p19Arf expression. Taken together, we show that increased ΔNp63α protein levels facilitate oncogenic transformation in the epidermis as well as in the bile duct.
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Affiliation(s)
- Michael Devos
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Barbara Gilbert
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Geertrui Denecker
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Molecular and Cellular Oncology Unit, Inflammation Research Center, VIB, Ghent, Belgium
| | - Kirsten Leurs
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Conor Mc Guire
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Molecular Signal Transduction in Inflammation Unit, Inflammation Research Center, VIB, Ghent, Belgium
| | - Kelly Lemeire
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Inflammation Research Center, VIB, Ghent, Belgium
| | - Tino Hochepied
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Transgenic mice core facility, VIB, Ghent, Belgium
| | | | - Jo Lambert
- Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | | | - Louis Libbrecht
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jody Haigh
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Vascular Cell Biology Unit, Department for Molecular Biomedical Research, VIB, Ghent, Belgium
| | - Geert Berx
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; Molecular and Cellular Oncology Unit, Inflammation Research Center, VIB, Ghent, Belgium
| | - Saskia Lippens
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Peter Vandenabeele
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Wim Declercq
- Molecular Signaling and Cell Death Unit, Inflammation Research Center, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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48
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Kruglikov IL, Scherer PE. Skin aging: are adipocytes the next target? Aging (Albany NY) 2016; 8:1457-69. [PMID: 27434510 PMCID: PMC4993342 DOI: 10.18632/aging.100999] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 07/07/2016] [Indexed: 01/09/2023]
Abstract
Dermal white adipose tissue (dWAT) is increasingly appreciated as a special fat depot. The adipocytes in this depot exert a variety of unique effects on their surrounding cells and can undergo massive phenotypic changes. Significant modulation of dWAT content can be observed both in intrinsically and extrinsically aged skin. Specifically, skin that has been chronically photo-damaged displays a reduction of the dWAT volume, caused by the replacement of adipocytes by fibrotic structures. This is likely to be caused by the recently uncovered process described as "adipocyte-myofibroblast transition" (AMT). In addition, contributions of dermal adipocytes to the skin aging processes are also indirectly supported by spatial correlations between the prevalence of hypertrophic scarring and the appearance of signs of skin aging in different ethnic groups. These observations could elevate dermal adipocytes to prime targets in strategies aimed at counteracting skin aging.
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Affiliation(s)
| | - Philipp E. Scherer
- Touchstone Diabetes Center, Departments of Internal Medicine and Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
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49
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Lee BH, Lee JS, Kim YC. Hair Growth-Promoting Effects of Lavender Oil in C57BL/6 Mice. Toxicol Res 2016; 32:103-8. [PMID: 27123160 PMCID: PMC4843973 DOI: 10.5487/tr.2016.32.2.103] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/15/2015] [Accepted: 12/22/2015] [Indexed: 11/20/2022] Open
Abstract
The purpose of this study was to determine the hair growth effects of lavender oil (LO) in female C57BL/6 mice. The experimental animals were divided into a normal group (N: saline), a vehicle control group (VC: jojoba oil), a positive control group (PC: 3% minoxidil), experimental group 1 (E1: 3% LO), and experimental group 2 (E2: 5% LO). Test compound solutions were topically applied to the backs of the mice (100 μL per application), once per day, 5 times a week, for 4 weeks. The changes in hair follicle number, dermal thickness, and hair follicle depth were observed in skin tissues stained with hematoxylin and eosin, and the number of mast cells was measured in the dermal and hypodermal layers stained with toluidine blue. PC, E1, and E2 groups showed a significantly increased number of hair follicles, deepened hair follicle depth, and thickened dermal layer, along with a significantly decreased number of mast cells compared to the N group. These results indicated that LO has a marked hair growth-promoting effect, as observed morphologically and histologically. There was no significant difference in the weight of the thymus among the groups. However, both absolute and relative weights of the spleen were significantly higher in the PC group than in the N, VC, E1, or E2 group at week 4. Thus, LO could be practically applied as a hair growth-promoting agent.
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Affiliation(s)
- Boo Hyeong Lee
- Department of Beauty Art, Changwon Moonsung University, Changwon, Korea
| | - Jae Soon Lee
- Department of Beauty Design, Gyongbuk Science College, Chilgok, Korea
| | - Young Chul Kim
- Department of Public Health, Keimyung University, Daegu, Korea
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50
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Teplyuk NM, Uhlmann EJ, Wong AHK, Karmali P, Basu M, Gabriely G, Jain A, Wang Y, Chiocca EA, Stephens R, Marcusson E, Yi M, Krichevsky AM. MicroRNA-10b inhibition reduces E2F1-mediated transcription and miR-15/16 activity in glioblastoma. Oncotarget 2016; 6:3770-83. [PMID: 25738367 PMCID: PMC4414152 DOI: 10.18632/oncotarget.3009] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 12/21/2014] [Indexed: 12/19/2022] Open
Abstract
MicroRNA-10b (miR-10b) is commonly elevated in glioblastoma (GBM), while not expressed in normal brain tissues. Targeted inhibition of miR-10b has pleiotropic effects on GBM derived cell lines, it reduces GBM growth in animal models, but does not affect normal neurons and astrocytes. This data raises the possibility of developing miR-10b-targeting GBM therapy. However, the mechanisms contributing to miR-10b-mediated glioma cell survival and proliferation are unexplored. We found that inhibition of miR-10b has distinct effects on specific glioma cell lines. In cells expressing high levels of tumor suppressor p21WAF1/Cip1, it represses E2F1-mediated transcription, leading to down-regulation of multiple E2F1 target genes encoding for S-phase specific proteins, epigenetic modulators, and miRNAs (e.g. miR-15/16), and thereby stalling progression through the S-phase of cell cycle. Subsequently, miR-15/16 activities are reduced and many of their direct targets are de-repressed, including ubiquitin ligase FBXW7 that destabilizes Cyclin E. Conversely, GBM cells expressing low p21 level, or after p21 knock-down, exhibit weaker or no E2F1 response to miR-10b inhibition. Comparative analysis of The Cancer Genome Atlas revealed a strong correlation between miR-10b and multiple E2F target genes in GBM and low-grade glioma. Taken together, these findings indicate that miR-10b regulates E2F1-mediated transcription in GBM, in a p21-dependent fashion.
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Affiliation(s)
- Nadiya M Teplyuk
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Erik J Uhlmann
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andus Hon-Kit Wong
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Meenakshi Basu
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Galina Gabriely
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anant Jain
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Yang Wang
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - E Antonio Chiocca
- Department of Neurosurgery, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Robert Stephens
- Cancer Research and Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | | | - Ming Yi
- Cancer Research and Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
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