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Arellano-Ballestero H, Zubiak A, Dally C, Orchard K, Alrubayyi A, Charalambous X, Michael M, Torrance R, Eales T, Das K, Tran MGB, Sabry M, Peppa D, Lowdell MW. Proteomic and phenotypic characteristics of memory-like natural killer cells for cancer immunotherapy. J Immunother Cancer 2024; 12:e008717. [PMID: 39032940 PMCID: PMC11261707 DOI: 10.1136/jitc-2023-008717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2024] [Indexed: 07/23/2024] Open
Abstract
BACKGROUND Human and mouse natural killer (NK) cells have been shown to develop memory-like function after short-term exposure to the cocktail of IL-12/15/18 or to overnight co-culture with some tumor cell lines. The resulting cells retain enhanced lytic ability for up to 7 days as well as after cryopreservation, and memory-like NK cells (mlNK) have been shown to induce complete remissions in patients with hematological malignancies. No single phenotype has been described for mlNK and the physiological changes induced by the short-term cytokine or tumor-priming which are responsible for these enhanced functions have not been fully characterized. Here, we have generated mlNK by cytokine and tumor-priming to find commonalities to better define the nature of NK cell "memory" in vitro and, for the first time, in vivo. METHODS We initiated mlNK in vitro from healthy donors with cytokines (initiated cytokine-induced memory-like (iCIML)-NK) and by tumor priming (TpNK) overnight and compared them by high-dimensional flow cytometry, proteomic and metabolomic profiling. As a potential mechanism of enhanced cytolytic function, we analyzed the avidity of binding of the mlNK to NK-resistant tumors (z-Movi). We generated TpNK from healthy donors and from cancer patients to determine whether mlNK generated by interaction with a single tumor type could enhance lytic activity. Finally, we used a replication-incompetent tumor cell line (INKmune) to treat patients with myeloid leukaemias to potentiate NK cell function in vivo. RESULTS Tumor-primed mlNK from healthy donors and patients with cancer showed increased cytotoxicity against multiple tumor cell lines in vitro, analogous to iCIML-NK cells. Multidimensional cytometry identified distinct memory-like profiles of subsets of cells with memory-like characteristics; upregulation of CD57, CD69, CD25 and ICAM1. Proteomic profiling identified 41 proteins restricted to mlNK cells and we identified candidate molecules for the basis of NK memory which can explain how mlNK overcome inhibition by resistant tumors. Finally, of five patients with myelodysplastic syndrome or refractory acute myeloid leukemia treated with INKmune, three responded to treatment with measurable increases in NK lytic function and systemic cytokines. CONCLUSIONS NK cell "memory" is a physiological state associated with resistance to MHC-mediated inhibition, increased metabolic function, mitochondrial fitness and avidity to NK-resistant target cells.
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Affiliation(s)
| | - Agnieszka Zubiak
- Cancer Institute, University College London, London, UK
- INmuneBio Inc, Boca Raton, Florida, USA
| | - Chris Dally
- Department of Haematology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | - Kim Orchard
- Department of Haematology, University Hospital Southampton NHS Foundation Trust, Southampton, UK
| | | | | | | | | | - Trinity Eales
- Cancer Institute, University College London, London, UK
| | | | - Maxine G. B. Tran
- Department of Biotechnology, Division of Surgery and Interventional Science, University College London, London, UK
- Specialist Centre for Kidney Cancer, Royal Free Hospital, London, UK
| | - May Sabry
- Cancer Institute, University College London, London, UK
- INmuneBio Inc, Boca Raton, Florida, USA
| | - Dimitra Peppa
- Institute for Immunity and Transplantation, Division of Infection and Immunity, University College London, London, UK
| | - Mark W. Lowdell
- Cancer Institute, University College London, London, UK
- INmuneBio Inc, Boca Raton, Florida, USA
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Nshanian M, Geller BS, Gruber JJ, Chleilat F, Camarillo JM, Kelleher NL, Zhao Y, Snyder MP. Short-chain fatty acids propionate and butyrate control growth and differentiation linked to cellular metabolism. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.11.575111. [PMID: 38293216 PMCID: PMC10827076 DOI: 10.1101/2024.01.11.575111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The short-chain fatty acids (SCFA) propionate and butyrate are produced in large amounts by microbial metabolism and have been identified as unique acyl lysine histone marks. In order to better understand the function of these modifications we used ChIP-seq to map the genome-wide location of four short-chain acyl histone marks H3K18pr/bu and H4K12pr/bu in treated and untreated colorectal cancer (CRC) and normal cells, as well as in mouse intestines in vivo . We correlate these marks with open chromatin regions along with gene expression to access the function of the target regions. Our data demonstrate that propionate and butyrate act as promoters of growth, differentiation as well as ion transport. We propose a mechanism involving direct modification of specific genomic regions, resulting in increased chromatin accessibility, and in case of butyrate, opposing effects on the proliferation of normal versus CRC cells.
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Kossack ME, Tian L, Bowie K, Plavicki JS. Defining the cellular complexity of the zebrafish bipotential gonad. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.18.524593. [PMID: 36712047 PMCID: PMC9882255 DOI: 10.1101/2023.01.18.524593] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Zebrafish are routinely used to model reproductive development, function, and disease, yet we still lack a clear understanding of the fundamental steps that occur during early bipotential gonad development, including when endothelial cells, pericytes, and macrophage cells arrive at the bipotential gonad to support gonad growth and differentiation. Here, we use a combination of transgenic reporters and single-cell sequencing analyses to define the arrival of different critical cell types to the larval zebrafish gonad. We determined that blood initially reaches the gonad via a vessel formed from the swim bladder artery, which we have termed the gonadal artery. We find that vascular and lymphatic development occurs concurrently in the bipotential zebrafish gonad and our data suggest that similar to what has been observed in developing zebrafish embryos, lymphatic endothelial cells in the gonad may be derived from vascular endothelial cells. We mined preexisting sequencing data sets to determine whether ovarian pericytes had unique gene expression signatures. We identified 215 genes that were uniquely expressed in ovarian pericytes that were not expressed in larval pericytes. Similar to what has been shown in the mouse ovary, our data suggest that pdgfrb+ pericytes may support the migration of endothelial tip cells during ovarian angiogenesis. Using a macrophage-driven photoconvertible protein, we found that macrophage established a nascent resident population as early as 12 dpf and can be observed removing cellular material during gonadal differentiation. This foundational information demonstrates that the early bipotential gonad contains complex cellular interactions, which likely shape the health and function of the mature, differentiated gonad.
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Roka K, Solomou EE, Kattamis A. Telomere biology: from disorders to hematological diseases. Front Oncol 2023; 13:1167848. [PMID: 37274248 PMCID: PMC10235513 DOI: 10.3389/fonc.2023.1167848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 05/02/2023] [Indexed: 06/06/2023] Open
Abstract
Variations in the length of telomeres and pathogenic variants involved in telomere length maintenance have been correlated with several human diseases. Recent breakthroughs in telomere biology knowledge have contributed to the identification of illnesses named "telomeropathies" and revealed an association between telomere length and disease outcome. This review emphasizes the biology and physiology aspects of telomeres and describes prototype diseases in which telomeres are implicated in their pathophysiology. We also provide information on the role of telomeres in hematological diseases ranging from bone marrow failure syndromes to acute and chronic leukemias.
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Affiliation(s)
- Kleoniki Roka
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National & Kapodistrian University of Athens, “Aghia Sophia” Children’s Hospital, Full Member of ERN GENTURIS, Athens, Greece
| | - Elena E. Solomou
- Department of Internal Medicine, University of Patras Medical School, Rion, Greece
| | - Antonis Kattamis
- Division of Pediatric Hematology-Oncology, First Department of Pediatrics, National & Kapodistrian University of Athens, “Aghia Sophia” Children’s Hospital, Full Member of ERN GENTURIS, Athens, Greece
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5
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Guo J, Huang X, Dou L, Yan M, Shen T, Tang W, Li J. Aging and aging-related diseases: from molecular mechanisms to interventions and treatments. Signal Transduct Target Ther 2022; 7:391. [PMID: 36522308 PMCID: PMC9755275 DOI: 10.1038/s41392-022-01251-0] [Citation(s) in RCA: 211] [Impact Index Per Article: 105.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/03/2022] [Accepted: 11/10/2022] [Indexed: 12/23/2022] Open
Abstract
Aging is a gradual and irreversible pathophysiological process. It presents with declines in tissue and cell functions and significant increases in the risks of various aging-related diseases, including neurodegenerative diseases, cardiovascular diseases, metabolic diseases, musculoskeletal diseases, and immune system diseases. Although the development of modern medicine has promoted human health and greatly extended life expectancy, with the aging of society, a variety of chronic diseases have gradually become the most important causes of disability and death in elderly individuals. Current research on aging focuses on elucidating how various endogenous and exogenous stresses (such as genomic instability, telomere dysfunction, epigenetic alterations, loss of proteostasis, compromise of autophagy, mitochondrial dysfunction, cellular senescence, stem cell exhaustion, altered intercellular communication, deregulated nutrient sensing) participate in the regulation of aging. Furthermore, thorough research on the pathogenesis of aging to identify interventions that promote health and longevity (such as caloric restriction, microbiota transplantation, and nutritional intervention) and clinical treatment methods for aging-related diseases (depletion of senescent cells, stem cell therapy, antioxidative and anti-inflammatory treatments, and hormone replacement therapy) could decrease the incidence and development of aging-related diseases and in turn promote healthy aging and longevity.
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Affiliation(s)
- Jun Guo
- grid.506261.60000 0001 0706 7839The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730 China
| | - Xiuqing Huang
- grid.506261.60000 0001 0706 7839The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730 China
| | - Lin Dou
- grid.506261.60000 0001 0706 7839The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730 China
| | - Mingjing Yan
- grid.506261.60000 0001 0706 7839The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730 China
| | - Tao Shen
- grid.506261.60000 0001 0706 7839The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730 China
| | - Weiqing Tang
- grid.506261.60000 0001 0706 7839The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730 China
| | - Jian Li
- grid.506261.60000 0001 0706 7839The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology of National Health Commission, Beijing, 100730 China
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Mishra R, Haldar S, Biondi S, Bhari VK, Singh G, Bhowmick NA. TGF-β controls stromal telomere length through epigenetic modifications. 3 Biotech 2022; 12:290. [PMID: 36276465 PMCID: PMC9512944 DOI: 10.1007/s13205-022-03346-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/01/2022] [Indexed: 11/01/2022] Open
Abstract
Telomere length is primarily controlled by the enzyme telomerase, but being chromatin structures, telomeres undergo epigenetic regulation for their maintenance and function. Altered telomere length among cancer cells combined with shorter telomere length in cancer-associated stromal cells, strongly implicated with progression to prostate cancer metastasis and cancer death and providing a novel target for therapeutics. Transforming growth factor-β (TGF-β) signaling pathways are well-recognized for their role in stromal-epithelial interactions responsible for prostate androgen responsiveness, promoting tumorigenesis. However, the underlying mechanism remains unclear. We sought to establish a role for TGF-β in the regulation of telomere length in mouse and human prostate fibroblast. Polymerase chain reaction (PCR)-based telomere length measuring methods are widely used due to their repeatability and reproducibility. Using real-time RT-PCR-based telomere length measuring method, we identified that TGF-beta regulates telomere length via increased expression of histone methyltransferase, Suv39h1, which in turn affected histone methylation levels at the telomeric ends. Moreover, treatment of DAPT and non-steroidal antiandrogen bicalutamide demonstrated that notch and androgen signaling co-operated with TGF-ß in regulating stromal telomere length. Telomere variation in tumor cells and non-tumor cells within the tumor microenvironment greatly facilitates the clinical assessment of prostate cancer; therefore, understanding stromal telomere length regulation mechanism will hold significant prospects for cancer treatment, diagnosis, and prognosis. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03346-5.
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Affiliation(s)
- Rajeev Mishra
- Department of Life Sciences and Biotechnology, Chhatrapati Shahu Ji Maharaj University, Kalyanpur, Kanpur, UP 208024 India
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Subhash Haldar
- Department of Food and Nutrition, University of Gour Banga, Mokdumpur, West Bengal 732101 India
| | - Shea Biondi
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
| | - Vikash Kumar Bhari
- Department of Biosciences, Manipal University Jaipur, Jaipur, Rajasthan 303007 India
| | - Gyanendra Singh
- Toxicology Department, ICMR-National Institute of Occupational Health, Ahmedabad, 380016 India
| | - Neil A Bhowmick
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048 USA
- Department of Research, Greater Los Angeles Veterans Administration, Los Angeles, CA 90073 USA
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7
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Wilson C, Murnane JP. High-throughput screen to identify compounds that prevent or target telomere loss in human cancer cells. NAR Cancer 2022; 4:zcac029. [PMID: 36196242 PMCID: PMC9527662 DOI: 10.1093/narcan/zcac029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/09/2022] [Accepted: 09/29/2022] [Indexed: 11/14/2022] Open
Abstract
Chromosome instability (CIN) is an early step in carcinogenesis that promotes tumor cell progression and resistance to therapy. Using plasmids integrated adjacent to telomeres, we have previously demonstrated that the sensitivity of subtelomeric regions to DNA double-strand breaks (DSBs) contributes to telomere loss and CIN in cancer. A high-throughput screen was created to identify compounds that affect telomere loss due to subtelomeric DSBs introduced by I-SceI endonuclease, as detected by cells expressing green fluorescent protein (GFP). A screen of a library of 1832 biologically-active compounds identified a variety of compounds that increase or decrease the number of GFP-positive cells following activation of I-SceI. A curated screen done in triplicate at various concentrations found that inhibition of classical nonhomologous end joining (C-NHEJ) increased DSB-induced telomere loss, demonstrating that C-NHEJ is functional in subtelomeric regions. Compounds that decreased DSB-induced telomere loss included inhibitors of mTOR, p38 and tankyrase, consistent with our earlier hypothesis that the sensitivity of subtelomeric regions to DSBs is a result of inappropriate resection during repair. Although this assay was also designed to identify compounds that selectively target cells experiencing telomere loss and/or chromosome instability, no compounds of this type were identified in the current screen.
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Affiliation(s)
- Chris Wilson
- Department of Pharmaceutical Chemistry, Small Molecule Discovery Center, University of California, San Francisco, CA 94143, USA
| | - John P Murnane
- To whom correspondence should be addressed. Tel: +1 415 680 4434;
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8
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Li B. Keeping Balance Between Genetic Stability and Plasticity at the Telomere and Subtelomere of Trypanosoma brucei. Front Cell Dev Biol 2021; 9:699639. [PMID: 34291053 PMCID: PMC8287324 DOI: 10.3389/fcell.2021.699639] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 06/08/2021] [Indexed: 12/13/2022] Open
Abstract
Telomeres, the nucleoprotein complexes at chromosome ends, are well-known for their essential roles in genome integrity and chromosome stability. Yet, telomeres and subtelomeres are frequently less stable than chromosome internal regions. Many subtelomeric genes are important for responding to environmental cues, and subtelomeric instability can facilitate organismal adaptation to extracellular changes, which is a common theme in a number of microbial pathogens. In this review, I will focus on the delicate and important balance between stability and plasticity at telomeres and subtelomeres of a kinetoplastid parasite, Trypanosoma brucei, which causes human African trypanosomiasis and undergoes antigenic variation to evade the host immune response. I will summarize the current understanding about T. brucei telomere protein complex, the telomeric transcript, and telomeric R-loops, focusing on their roles in maintaining telomere and subtelomere stability and integrity. The similarities and differences in functions and underlying mechanisms of T. brucei telomere factors will be compared with those in human and yeast cells.
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Affiliation(s)
- Bibo Li
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological, and Environmental Sciences, College of Sciences and Health Professions, Cleveland State University, Cleveland, OH, United States.,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States.,Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States.,Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH, United States
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9
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Telomere Shortening and Fusions: A Link to Aneuploidy in Early Human Embryo Development. Obstet Gynecol Surv 2021; 76:429-436. [PMID: 34324695 DOI: 10.1097/ogx.0000000000000907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Importance It is known that oocytes undergo aging that is caused by exposure to an aged ovarian microenvironment. Telomere length in mouse and bovine oocytes declines with age, and age-associated telomere shortening in oocytes is considered a sign of poor development competency. Women with advanced age undergoing assisted reproductive technologies have poor outcomes because of increasing aneuploidy rates with age. Research has shown that aneuploidy is associated with DNA damage, reactive oxygen species, and telomere dysfunction. Objective In this review, we focus on the possible relationship between telomere dysfunction and aneuploidy in human early embryo development and several reproductive and perinatal outcomes, discussing the mechanism of aneuploidy caused by telomere shortening and fusion in human embryos. Evidence Acquisition We reviewed the current literature evidence concerning telomere dysfunction and aneuploidy in early human embryo development. Results Shorter telomeres in oocytes, leukocytes, and granulosa cells, related to aging in women, were associated with recurrent miscarriage, trisomy 21, ovarian insufficiency, and decreasing chance of in vitro fertilization success. Telomere length and telomerase activity in embryos have been related to the common genomic instability at the cleavage stage of human development. Complications of assisted reproductive technology pregnancies, such as miscarriage, birth defects, preterm births, and intrauterine growth restriction, also might result from telomere shortening as observed in oocytes, polar body, granulosa cells, and embryos. Conclusions and Relevance Telomere length clearly plays an important role in the development of the embryo and fetus, and the abnormal shortening of telomeres is likely involved in embryo loss during early human development. However, telomere fusion studies have yet to be performed in early human development.
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10
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Tobias PA, Schwessinger B, Deng CH, Wu C, Dong C, Sperschneider J, Jones A, Lou Z, Zhang P, Sandhu K, Smith GR, Tibbits J, Chagné D, Park RF. Austropuccinia psidii, causing myrtle rust, has a gigabase-sized genome shaped by transposable elements. G3 (BETHESDA, MD.) 2021; 11:jkaa015. [PMID: 33793741 PMCID: PMC8063080 DOI: 10.1093/g3journal/jkaa015] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 10/26/2020] [Indexed: 02/06/2023]
Abstract
Austropuccinia psidii, originating in South America, is a globally invasive fungal plant pathogen that causes rust disease on Myrtaceae. Several biotypes are recognized, with the most widely distributed pandemic biotype spreading throughout the Asia-Pacific and Oceania regions over the last decade. Austropuccinia psidii has a broad host range with more than 480 myrtaceous species. Since first detected in Australia in 2010, the pathogen has caused the near extinction of at least three species and negatively affected commercial production of several Myrtaceae. To enable molecular and evolutionary studies into A. psidii pathogenicity, we assembled a highly contiguous genome for the pandemic biotype. With an estimated haploid genome size of just over 1 Gb (gigabases), it is the largest assembled fungal genome to date. The genome has undergone massive expansion via distinct transposable element (TE) bursts. Over 90% of the genome is covered by TEs predominantly belonging to the Gypsy superfamily. These TE bursts have likely been followed by deamination events of methylated cytosines to silence the repetitive elements. This in turn led to the depletion of CpG sites in TEs and a very low overall GC content of 33.8%. Compared to other Pucciniales, the intergenic distances are increased by an order of magnitude indicating a general insertion of TEs between genes. Overall, we show how TEs shaped the genome evolution of A. psidii and provide a greatly needed resource for strategic approaches to combat disease spread.
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Affiliation(s)
- Peri A Tobias
- School of Life and Environmental Sciences, University of Sydney, Camperdown, NSW 2006, Australia
- Plant & Food Research Australia, SA 5064, Australia
| | - Benjamin Schwessinger
- Australia Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Cecilia H Deng
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Chen Wu
- The New Zealand Institute for Plant and Food Research Limited, Auckland 1142, New Zealand
| | - Chongmei Dong
- Plant Breeding Institute, University of Sydney, Narellan, NSW 2567, Australia
| | - Jana Sperschneider
- Biological Data Science Institute, The Australian National University, Canberra, ACT, 2600, Australia
| | - Ashley Jones
- Australia Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Zhenyan Lou
- Australia Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Peng Zhang
- Plant Breeding Institute, University of Sydney, Narellan, NSW 2567, Australia
| | - Karanjeet Sandhu
- Plant Breeding Institute, University of Sydney, Narellan, NSW 2567, Australia
| | - Grant R Smith
- The New Zealand Institute for Plant and Food Research Limited, Christchurch 8140, New Zealand
| | - Josquin Tibbits
- Agriculture Victoria Department of Jobs, Precincts and Regions, Bundoora, VIC 3083, Australia
| | - David Chagné
- The New Zealand Institute for Plant & Food Research, Palmerston North 4442, New Zealand
| | - Robert F Park
- Plant Breeding Institute, University of Sydney, Narellan, NSW 2567, Australia
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11
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Peron A, Catusi I, Recalcati MP, Calzari L, Larizza L, Vignoli A, Canevini MP. Ring Chromosome 20 Syndrome: Genetics, Clinical Characteristics, and Overlapping Phenotypes. Front Neurol 2020; 11:613035. [PMID: 33363513 PMCID: PMC7753021 DOI: 10.3389/fneur.2020.613035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 11/09/2020] [Indexed: 12/15/2022] Open
Abstract
Ring chromosome 20 [r(20)] syndrome is a rare condition characterized by a non-supernumerary ring chromosome 20 replacing a normal chromosome 20. It is commonly seen in a mosaic state and is diagnosed by means of karyotyping. r(20) syndrome is characterized by a recognizable epileptic phenotype with typical EEG pattern, intellectual disability manifesting after seizure onset in otherwise normally developing children, and behavioral changes. Despite the distinctive phenotype, many patients still lack a diagnosis-especially in the genomic era-and the pathomechanisms of ring formation are poorly understood. In this review we address the genetic and clinical aspects of r(20) syndrome, and discuss differential diagnoses and overlapping phenotypes, providing the reader with useful tools for clinical and laboratory practice. We also discuss the current issues in understanding the mechanisms through which ring 20 chromosome causes the typical manifestations, and present unpublished data about methylation studies. Ultimately, we explore future perspectives of r(20) research. Our intended audience is clinical and laboratory geneticists, child and adult neurologists, and genetic counselors.
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Affiliation(s)
- Angela Peron
- Human Pathology and Medical Genetics, ASST Santi Paolo e Carlo, San Paolo Hospital, Milan, Italy.,Child Neuropsychiatry Unit - Epilepsy Center, Department of Health Sciences, ASST Santi Paolo e Carlo, San Paolo Hospital, Università Degli Studi di Milano, Milan, Italy.,Division of Medical Genetics, Department of Pediatrics, University of Utah School of Medicine, Salt Lake City, UT, United States
| | - Ilaria Catusi
- Laboratory of Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano IRCCS-Istituto di Ricovero e Cura a Carattere Scientifico, Cusano Milanino, Milan, Italy
| | - Maria Paola Recalcati
- Laboratory of Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano IRCCS-Istituto di Ricovero e Cura a Carattere Scientifico, Cusano Milanino, Milan, Italy
| | - Luciano Calzari
- Bioinformatics and Statistical Genomics Unit, Istituto Auxologico Italiano IRCCS-Istituto di Ricovero e Cura a Carattere Scientifico, Cusano Milanino, Milan, Italy
| | - Lidia Larizza
- Laboratory of Cytogenetics and Molecular Genetics, Istituto Auxologico Italiano IRCCS-Istituto di Ricovero e Cura a Carattere Scientifico, Cusano Milanino, Milan, Italy
| | - Aglaia Vignoli
- Child Neuropsychiatry Unit - Epilepsy Center, Department of Health Sciences, ASST Santi Paolo e Carlo, San Paolo Hospital, Università Degli Studi di Milano, Milan, Italy
| | - Maria Paola Canevini
- Child Neuropsychiatry Unit - Epilepsy Center, Department of Health Sciences, ASST Santi Paolo e Carlo, San Paolo Hospital, Università Degli Studi di Milano, Milan, Italy
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12
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Essentiality of CTNNB1 in Malignant Transformation of Human Embryonic Stem Cells under Long-Term Suboptimal Conditions. Stem Cells Int 2020; 2020:5823676. [PMID: 33029148 PMCID: PMC7532415 DOI: 10.1155/2020/5823676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/14/2020] [Accepted: 08/28/2020] [Indexed: 12/12/2022] Open
Abstract
Human embryonic stem cells (hESCs) gradually accumulate abnormal karyotypes during long-term suboptimal culture, which hinder their application in regenerative medicine. Previous studies demonstrated that the activation of CTNNB1 might be implicated in this process. Hence, the hESC line with stably silenced CTNNB1 was established to further explore the role of CTNNB1 in the malignant transformation of hESCs. It was shown to play a vital role in the maintenance of the physiological properties of stem cells, such as proliferation, migration, differentiation, and telomere regulation. Furthermore, the malignant transformation of hESCs was induced by continuous exposure to 0.001 μg/ml mitomycin C (MMC). The results showed that CTNNB1 and its target genes, including proto-oncogenes CCND1 and C-MYC, were aberrantly upregulated in hESCs after MMC treatment. Moreover, the high expression of CTNNB1 accelerated cell transition from G0/G1 phase to the S phase and stimulated the growth of cells containing breakage-fusion-bridge (BFB) cycles. Conversely, CTNNB1 silencing inhibited these effects and triggered a survival crisis. The current data indicated that CTNNB1 is intimately associated with the physiological properties of stem cells; however, the aberrant expression of CTNNB1 is involved in the malignant transformation of hESCs, which might advance the process by facilitating telomere-related unstable cell proliferation. Thus, the aberrant CTNNB1 level might serve as a potential biomarker for detecting the malignant transformation of hESCs.
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DNA methylation in satellite repeats disorders. Essays Biochem 2020; 63:757-771. [PMID: 31387943 DOI: 10.1042/ebc20190028] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 02/06/2023]
Abstract
Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.
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14
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Fossel M. A unified model of dementias and age-related neurodegeneration. Alzheimers Dement 2020; 16:365-383. [PMID: 31943780 DOI: 10.1002/alz.12012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/09/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
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15
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Yudin NS, Belyavskaya VA, Maksimov VN, Ivanoshchuk DE, Orlov PS, Voevoda MI. Association between leukocyte telomere length and specific antibody levels after vaccination against tick-borne encephalitis. Vavilovskii Zhurnal Genet Selektsii 2020. [DOI: 10.18699/vj19.580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- N. S. Yudin
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Research Institute of Internal and Preventive Medicine
| | - V. A. Belyavskaya
- State Research Center of Virology and Biotechnology “Vector” of the Federal Service for Surveillance in Consumer Rights Protection and Human Well-being
| | - V. N. Maksimov
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Research Institute of Internal and Preventive Medicine
| | - D. E. Ivanoshchuk
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Research Institute of Internal and Preventive Medicine
| | - P. S. Orlov
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Research Institute of Internal and Preventive Medicine
| | - M. I. Voevoda
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University; Research Institute of Internal and Preventive Medicine
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16
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Hognon C, Gebus A, Barone G, Monari A. Human DNA Telomeres in Presence of Oxidative Lesions: The Crucial Role of Electrostatic Interactions on the Stability of Guanine Quadruplexes. Antioxidants (Basel) 2019; 8:antiox8090337. [PMID: 31443537 PMCID: PMC6770428 DOI: 10.3390/antiox8090337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 01/23/2023] Open
Abstract
By using all atom molecular dynamics simulations, we studied the behavior of human DNA telomere sequences in guanine quadruplex (G4) conformation and in the presence of oxidative lesions, namely abasic sites. In particular, we evidenced that while removing one guanine base induces a significant alteration and destabilization of the involved leaflet, human telomere oligomers tend, in most cases, to maintain at least a partial quadruplex structure, eventually by replacing the empty site with undamaged guanines of different leaflets. This study shows that (i) the disruption of the quadruplex leaflets induces the release of at least one of the potassium cations embedded in the quadruplex channel and that (ii) the electrostatic interactions of the DNA sequence with the aforementioned cations are fundamental to the maintenance of the global quadruplex structure.
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Affiliation(s)
- Cecilia Hognon
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
| | - Adrien Gebus
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France
| | - Giampaolo Barone
- Department of Biological, Chenical and Pharmaceutical Sciences and Technologies, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Antonio Monari
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
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17
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Nguyen K, Broucqsault N, Chaix C, Roche S, Robin JD, Vovan C, Gerard L, Mégarbané A, Urtizberea JA, Bellance R, Barnérias C, David A, Eymard B, Fradin M, Manel V, Sacconi S, Tiffreau V, Zagnoli F, Cuisset JM, Salort-Campana E, Attarian S, Bernard R, Lévy N, Magdinier F. Deciphering the complexity of the 4q and 10q subtelomeres by molecular combing in healthy individuals and patients with facioscapulohumeral dystrophy. J Med Genet 2019; 56:590-601. [PMID: 31010831 DOI: 10.1136/jmedgenet-2018-105949] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 02/28/2019] [Accepted: 03/24/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND Subtelomeres are variable regions between telomeres and chromosomal-specific regions. One of the most studied pathologies linked to subtelomeric imbalance is facioscapulohumeral dystrophy (FSHD). In most cases, this disease involves shortening of an array of D4Z4 macrosatellite elements at the 4q35 locus. The disease also segregates with a specific A-type haplotype containing a degenerated polyadenylation signal distal to the last repeat followed by a repetitive array of β-satellite elements. This classification applies to most patients with FSHD. A subset of patients called FSHD2 escapes this definition and carries a mutation in the SMCHD1 gene. We also recently described patients carrying a complex rearrangement consisting of a cis-duplication of the distal 4q35 locus identified by molecular combing. METHODS Using this high-resolution technology, we further investigated the organisation of the 4q35 region linked to the disease and the 10q26 locus presenting with 98% of homology in controls and patients. RESULTS Our analyses reveal a broad variability in size of the different elements composing these loci highlighting the complexity of these subtelomeres and the difficulty for genomic assembly. Out of the 1029 DNA samples analysed in our centre in the last 7 years, we also identified 54 cases clinically diagnosed with FSHD carrying complex genotypes. This includes mosaic patients, patients with deletions of the proximal 4q region and 23 cases with an atypical chromosome 10 pattern, infrequently found in the control population and never reported before. CONCLUSION Overall, this work underlines the complexity of these loci challenging the diagnosis and genetic counselling for this disease.
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Affiliation(s)
- Karine Nguyen
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Natacha Broucqsault
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Charlene Chaix
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Stephane Roche
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Jérôme D Robin
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Catherine Vovan
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Laurene Gerard
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France
| | | | - Jon Andoni Urtizberea
- Pôle Soins de suite et réadaptation handicaps lourds et maladies rares neurologiques, Hôpital Marin, Assistance publique des hopitaux de Paris, Hendaye, France
| | - Remi Bellance
- Hopital Pierre Zobda-Quitman, Fort-de-France, France
| | - Christine Barnérias
- Service de Neurologie infantile, Université Paris Descartes, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France.,Centre de Référence de Maladies Neuromusculaires Garches-Necker-Mondor-Hendaye (GNMH), Réseau National Français de la Filière Neuromusculaire (FILNEMUS), Paris, France
| | | | - Bruno Eymard
- Assistance Publique - Hopitaux de Paris, Paris, Île-de-France, France
| | - Melanie Fradin
- Service de Génétique Médicale, Centre De Référence Anomalies du Développement, CHU de Rennes, Rennes, France
| | - Véronique Manel
- Centre référent maladies neuromusculaires rares, Hospices Civils de Lyon, Hôpital Femme Mère Enfant, Bron, France
| | - Sabrina Sacconi
- Peripheral Nervous System, Muscle and ALS Department, Université Côte d'Azur, Nice, France.,Institute for Research on Cancer and Aging of Nice, Université Côte d'Azur, Faculty of Medicine, Nice, France
| | - Vincent Tiffreau
- Centre de Référence des Maladies Neuromusculaires, service de Médecine Physique et de Réadaptation, Centre hospitalier régionale de Lille, Lille, France
| | - Fabien Zagnoli
- Centre de Référence des Maladies Neuromusculaires, CHU Morvan, Brest, France
| | | | - Emmanuelle Salort-Campana
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France.,Centre de reference des maladies neuromusculaires, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Shahram Attarian
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France.,Centre de reference des maladies neuromusculaires, Assistance Publique Hopitaux de Marseille, Marseille, France
| | - Rafaëlle Bernard
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Nicolas Lévy
- Medical Genetics, Assistance Publique Hopitaux de Marseille, Marseille, France.,Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
| | - Frederique Magdinier
- Aix Marseille Univ, INSERM, MMG, Marseille Medical Genetics U1251, Marseille, France
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